Abstract
Transcription is controlled by multi-protein complexes binding to short non-coding regions of genomic DNA. These complexes interact combinatorially. A major goal of modern biology is to provide simple models that predict this complex behavior. The yeast gene RNR1 is transcribed periodically during the cell cycle. Here, we present a pilot study to demonstrate a new method of deciphering the logic behind transcriptional regulation. We took regular samples from cell cycle synchronized cultures of Saccharomyces cerevisiae and extracted nuclear protein. We tested these samples to measure the amount of protein that bound to seven different 16 base pair sequences of DNA that have been previously identified as protein binding locations in the promoter of the RNR1 gene. These tests were performed using surface plasmon resonance. We found that the surface plasmon resonance signals showed significant variation throughout the cell cycle. We correlated the protein binding data with previously published mRNA expression data and interpreted this to show that transcription requires protein bound to a particular site and either five different sites or one additional sites. We conclude that this demonstrates the feasibility of this approach to decipher the combinatorial logic of transcription.
Highlights
IntroductionSpecific DNA sequences can regulate gene expression
Proteins binding to short, specific DNA sequences can regulate gene expression
We demonstrated that we can monitor dynamic changes in the occupancy of regulatory elements by monitoring yeast nuclear protein binding to a region of the RNR1 promoter as the cell cycle progresses [25]
Summary
Specific DNA sequences can regulate gene expression. These proteins, called transcription factors, enhance or repress transcription. Transcription factor binding sites are generally short (less than 12 base pairs) in length and are usually located in the promoter region of the regulated gene. The binding of a single protein to the gene’s promoter can enhance or repress expression. Expression is regulated through a combination of multiprotein complexes binding to several distinct elements. The determination of the location and decoding of the combinatorial logic of all these regulatory elements would provide an important annotation to the complete genome sequence and could lead to a better understanding of development and evolution [1,2,3,4]
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