Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis

Ryan K Shultzaberger,Alan M Moses,Michael B Eisen,Derek Y Chiang

doi:10.1371/journal.pone.0001199

Ryan K Shultzaberger, Alan M Moses + Show 2 more

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https://doi.org/10.1371/journal.pone.0001199

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Abstract

Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we can understand the “rules” that define functional cooperativity. Conversely, by understanding the rules of binding, we can infer structural characteristics. We have developed an information theory based method for approximating the physical limitations of cooperative interactions by comparing sequence analysis to microarray expression data. When applied to the coordinated binding of the sulfur amino acid regulatory protein Met4 by Cbf1 and Met31, we were able to create a combinatorial model that can correctly identify Met4 regulated genes. Interestingly, we found that the major determinant of Met4 regulation was the sum of the strength of the Cbf1 and Met31 binding sites and that the energetic costs associated with spacing appeared to be minimal.

Highlights

The regulation of transcriptional initiation from individual eukaryotic promoters is often controlled by multiple cooperatively interacting transcription factors
Deviation of sequence conservation from the helical accessibility wave is generally an indicator of structural changes in the DNA substrate [29]. This may be consistent with the observed bending of DNA by Cbf1 [30]
The Met31 model was built as described in Materials and Methods (Fig. 1B)

Summary

Introduction

The regulation of transcriptional initiation from individual eukaryotic promoters is often controlled by multiple cooperatively interacting transcription factors. These factors bind to separate sites in cis-regulatory sequences and physically interact with each other, either directly or through additional proteins, to activate or repress transcription [1,2,3]. These physical interactions among transcription factors must constrain how their binding sites can be positioned relative to each other and to the relevant promoters. Positioned sites presumably introduce clashes or strain into either the complex or DNA which will, in turn, reduce the stability of the complex

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