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Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA

By Dmitry B. Veprintsev and Alan R. Fersht

Abstract

The tumour suppressor p53 is a transcription factor that binds DNA in the vicinity of the genes it controls. The affinity of p53 for specific binding sites relative to other DNA sequences is an inherent driving force for specificity, all other things being equal. We measured the binding affinities of systematically mutated consensus p53 DNA-binding sequences using automated fluorescence anisotropy titrations. Based on measurements of the effects of every possible single base-pair substitution of a consensus sequence, we defined the DNA sequence with the highest affinity for full-length p53 and quantified the effects of deviation from it on the strength of protein–DNA interaction. The contributions of individual nucleotides were to a first approximation independent and additive. But, in some cases we observed significant deviations from additivity. Based on affinity data, we constructed a binding predictor that mirrored the existing p53 consensus sequence definition. We used it to search for high-affinity binding sites in the genome and to predict the effects of single-nucleotide polymorphisms in these sites. Although there was some correlation between the Kd and biological function, the spread of the Kds by itself was not sufficient to explain the activation of different pathways by changes in p53 concentration alone

Topics: Computational Biology
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:2275157
Provided by: PubMed Central
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    1. (2006). A global map of p53 transcription-factor binding sites in the human genome.
    2. (2002). Additivity in protein–DNA interactions: how good an approximation is it?
    3. (2007). An integrated map of p53-binding sites and histone modification in the human ENCODE regions.
    4. (2006). ChIP-chip comes of age for genome-wide functional analysis.
    5. (2005). Comparative binding of p53 to its promoter and DNA recognition elements.
    6. (2004). Cooperative binding of tetrameric p53 to DNA.
    7. (2006). Core domain interactions in full-length p53 in solution.
    8. (2004). Crystal structure of a superstable mutant of human p53 core domain: insights into the mechanism of rescuing oncogenic mutations.
    9. (1992). Definition of a consensus binding site for p53.
    10. (2005). DIP-chip: rapid and accurate determination of DNA-binding specificity.
    11. (2000). DNA binding sites: representation and discovery.
    12. (2006). DNA microarray technologies for measuring protein–DNA interactions.
    13. (2006). Effects of common cancer mutations on stability and DNA binding of fulllength p53 compared with isolated core domains.
    14. (2006). Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.
    15. (2002). Groups of p53 target genes involved in specific p53 downstream effects cluster into different classes of DNA binding sites.
    16. (2007). hCAS/ CSE1L associates with chromatin and regulates expression of select p53 target genes.
    17. (2001). Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.
    18. (2007). p53 in health and disease.
    19. (2005). Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.
    20. (1986). Quantitative analysis of the relationship between nucleotide sequence and functional activity.
    21. (2004). Quantitative high-throughput analysis of transcription factor binding specificities.
    22. (2002). Quantitative prediction of NF-kappa B DNA–protein interactions.
    23. (2002). Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities.
    24. (1987). Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    25. (1998). Semirational design of active tumor suppressor p53 DNA binding domain with enhanced stability.
    26. (2007). Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.
    27. (1990). Sequence logos: a new way to display consensus sequences.
    28. (2006). Structural basis of DNA recognition by p53 tetramers.
    29. (2000). Surfing the p53 network.
    30. (2007). The p53 knowledgebase: an integrated information resource for p53 research.
    31. (2004). Transcriptional regulatory code of a eukaryotic genome.
    32. (2004). Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

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