Abstract
Transcription factors that drive complex patterns of gene expression during animal development bind to thousands of genomic regions, with quantitative differences in binding across bound regions mediating their activity. While we now have tools to characterize the DNA affinities of these proteins and to precisely measure their genome-wide distribution in vivo, our understanding of the forces that determine where, when, and to what extent they bind remains primitive. Here we use a thermodynamic model of transcription factor binding to evaluate the contribution of different biophysical forces to the binding of five regulators of early embryonic anterior-posterior patterning in Drosophila melanogaster. Predictions based on DNA sequence and in vitro protein-DNA affinities alone achieve a correlation of ∼0.4 with experimental measurements of in vivo binding. Incorporating cooperativity and competition among the five factors, and accounting for spatial patterning by modeling binding in every nucleus independently, had little effect on prediction accuracy. A major source of error was the prediction of binding events that do not occur in vivo, which we hypothesized reflected reduced accessibility of chromatin. To test this, we incorporated experimental measurements of genome-wide DNA accessibility into our model, effectively restricting predicted binding to regions of open chromatin. This dramatically improved our predictions to a correlation of 0.6–0.9 for various factors across known target genes. Finally, we used our model to quantify the roles of DNA sequence, accessibility, and binding competition and cooperativity. Our results show that, in regions of open chromatin, binding can be predicted almost exclusively by the sequence specificity of individual factors, with a minimal role for protein interactions. We suggest that a combination of experimentally determined chromatin accessibility data and simple computational models of transcription factor binding may be used to predict the binding landscape of any animal transcription factor with significant precision.
Highlights
In vivo crosslinking studies show that animal transcription factors each bind to many thousands of DNA regions throughout the genome (e.g. [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18])
Factors with unrelated biochemical or functional properties bind to the same genomic regions with surprisingly high frequency [2,16,20], while the biological specificities of factors appear to be determined in part by quantitative differences in occupancy between proteins at these commonly bound sites [2,16,21,22]
This discrepancy between predicted and observed factor binding has been attributed to several mechanisms that could alter the simple behavior of a factor, including: (1) competitive inhibition of binding at those DNA regions that overlap sites occupied either by other sequence specific factors [26,27] or by nucleosomes and chromatin associated proteins [28,29,30,31,32,33]
Summary
In vivo crosslinking studies show that animal transcription factors each bind to many thousands of DNA regions throughout the genome (e.g. [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18]). Animal transcription factors bind to short (5–12 bp) sequences of DNA that occur with high frequency throughout the genome [23], yet most occurrences of these recognition sequences are not detectably bound in vivo [2,5,13,24,25]. This discrepancy between predicted and observed factor binding has been attributed to several mechanisms that could alter the simple behavior of a factor, including: (1) competitive inhibition of binding at those DNA regions that overlap sites occupied either by other sequence specific factors [26,27] or by nucleosomes and chromatin associated proteins [28,29,30,31,32,33]. The relative influence that each of these biochemical mechanisms on the overall pattern of factor binding in vivo, is currently a matter of debate
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