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Accurate and Sensitive Quantification of Protein-DNA Binding Affinity

Chaitanya Rastogi

Title:
Accurate and Sensitive Quantification of Protein-DNA Binding Affinity
Author(s):
Rastogi, Chaitanya
Thesis Advisor(s):
Bussemaker, Harmen J.
Bienstock, Daniel
Date:
Type:
Theses
Degree:
Ph.D., Columbia University
Department(s):
Applied Physics and Applied Mathematics
Persistent URL:
Abstract:
Transcription factors control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in transcription factor binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here we developed a versatile maximum likelihood framework, named No Read Left Behind (NRLB), that fits a biophysical model of protein-DNA recognition to all in vitro selected DNA binding sites across the full affinity range. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. The model captures the specificity of p53 tetrameric binding sites and discovers multiple binding modes in a single sample. Additionally, we confirm that newly-identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.
Subject(s):
Genetics
Biophysics
Statistics
DNA-protein interactions
Transcription factors
Item views
86
Metadata:
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Suggested Citation:
Chaitanya Rastogi, , Accurate and Sensitive Quantification of Protein-DNA Binding Affinity, Columbia University Academic Commons, .

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