Promoter-specific or all wRAPped up in the genome?

Abstract

A question that has puzzled biologists is ‘what determines where, when and how regulatory proteins bind to the genome?’ These DNA-binding proteins control the expression of specific genes and are of fundamental importance for eukaryotic cell growth and survival. In Saccharomyces cerevisiae, repressor activator protein 1 (Rap1) is one such protein, which, together with the accessory silencing proteins Sir2, Sir3 and Sir4, functions to regulate telomere length and mating. Independent of Sir proteins, Rap1 is an essential sequence-specific transcriptional regulator of many crucial S. cerevisiae genes, acting either directly as a transcriptional activator or as an accessory for binding by other regulatory proteins. By examining the specificity of Rap1–DNA binding across the entire yeast genome, Lieb et al. 1xSee all References1 now provide some interesting answers to this fundamental biological question.Yeast chromatin fragments enriched in stabilized Rap1 and Sir protein complexes were hybridized to DNA microarrays containing 12 943 DNA segments that represented every coding and intergenic region of the yeast genome. This novel approach enabled Lieb and colleagues to construct a genome-wide map of DNA–protein interactions. Careful analysis of the data identified the specific genomic targets of Rap1 and the Sir proteins. Consistent with the ability of these regulatory proteins to bind to telomeres, telomeric DNA was enriched in the Rap1 protein complexes.The analysis also allowed the identification of genes that Rap1 might regulate. To their delight, Lieb et al. found that Rap1 bound to the intergenic region immediately upstream of 362 genes. The protein products of these genes include ribosomal proteins, a continuous enzymatic pathway in glycolysis and others involved in protein synthesis. However, the most exciting finding was that, although the binding sequence for Rap1 occurs throughout the genome, Rap1 binds specifically to intergenic sequences containing potential promoters, rather than to coding sequences. This result raises the possibility that such a phenomenon might be a general property of proteins that function as transcriptional regulators but recognize DNA motifs found throughout the genome. There is no question that such a finding suggests the existence of a genome-wide mechanism that distinguishes between the potential DNA-binding sites that occur within coding regions and those in intergenic regions. The race is now on to understand how these promoter regions are ‘marked’. In the meantime, we eagerly await the results of the next study to use this powerful genomic mapping approach to identify the in vivo binding sites of other transcription factors with unknown DNA-binding specificities.