Transcriptional regulation usually requires specific interaction between transcription actor (TF) and DNA binding sequence; however, specific DNA binding sequence along is not sufficient to predict the actual transcription factor binding sites. Further, actual binding sites may not qualify as regulated genes. Therefore, with the same or similar binding sites, why some of them are regulated by the bound transcription factor and the others are not?
I'd like to address this question with the phosphate starvation response pathway of S. cerevisiae, which is regulated by transcription factors pho4 and pho2. Pho4 binding motif has been identified and the predicted pho4 binding sites distribute across yeast genome, with no significant difference between open reading frame and promoter region. Also, cofactor is important in selective regulation and in this case, pho2 and pho4 has been shown to physically interact to regulate transcriptional activation. Those two facts make PHO system a good example to study the question.
I will use microarray to identify the pho4 regulated and pho2 regulated genes, and then use chip-on-chip method to identify the in vivo binding sites for both pho4 and pho2. Combining the transcriptional level regulation profile with the physical interaction map, I want to answer: 1, how pho2 and pho4 cooperate to regulate phosphate starvation response. 2, with the same binding motif, why some genes are regulated by pho4 and others are not? To answer the second question, a nucleosome position map may also be required.
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