Nature Genetics Advance Online Publication: 16 July 2001, DOI:10.1038/ng569
"Promoter-Specific Binding of Rap1 Revealed by Genome-Wide Maps of Protein–DNA Association".
Jason D. Lieb 1, Xiaole Liu 2, David Botstein 3 & Patrick O. Brown 1
1 Department of Biochemistry, Stanford University, Stanford,
California 94305-5428, USA.
2 Stanford Medical Informatics, Stanford University,
Stanford, California 94305-5428, USA.
3 Department of Genetics, Stanford University, Stanford,
California 94305-5428, USA.
Correspondence should be addressed to P O Brown.
e-mail: pbrown@cmgm.stanford.edu
We determined the distribution of repressor-activator protein 1 (Rap1) and the accessory silencing proteins Sir2, Sir3 and Sir4 in vivo on the entire yeast genome, at a resolution of 2 kb. Rap1 is central to the cellular economy during rapid growth, targeting 294 loci, about 5% of yeast genes, and participating in the activation of 37% of all RNA polymerase II initiation events in exponentially growing cells. Although the DNA sequence recognized by Rap1 is found in both coding and intergenic sequences, the binding of Rap1 to the genome was highly specific to intergenic regions with the potential to act as promoters. This global phenomenon, which may be a general characteristic of sequence-specific transcriptional factors, indicates the existence of a genome-wide molecular mechanism for marking promoter regions.
1. "Activation of DNA Transcription within Repressed Chromatin by Nuclear RNA Species".
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