Guertin, M. J., Martins, A. L., Siepel, A., Lis, J. T. (2012) Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet, 8 (3). e1002610. ISSN 1553-7390
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Abstract
DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding followed by high-throughput sequencing (PB-seq), that allows the binding energy landscape to be characterized genome-wide in the absence of chromatin. We applied our methods to the Drosophila Heat Shock Factor (HSF), which inducibly binds a target DNA sequence element (HSE) following heat shock stress. PB-seq involves incubating sheared naked genomic DNA with recombinant HSF, partitioning the HSF-bound and HSF-free DNA, and then detecting HSF-bound DNA by high-throughput sequencing. We compared PB-seq binding profiles with ones observed in vivo by ChIP-seq and developed statistical models to predict the observed departures from idealized binding patterns based on covariates describing the local chromatin environment. We found that DNase I hypersensitivity and tetra-acetylation of H4 were the most influential covariates in predicting changes in HSF binding affinity. We also investigated the extent to which DNA accessibility, as measured by digital DNase I footprinting data, could be predicted from MNase-seq data and the ChIP-chip profiles for many histone modifications and TFs, and found GAGA element associated factor (GAF), tetra-acetylation of H4, and H4K16 acetylation to be the most predictive covariates. Lastly, we generated an unbiased model of HSF binding sequences, which revealed distinct biophysical properties of the HSF/HSE interaction and a previously unrecognized substructure within the HSE. These findings provide new insights into the interplay between the genomic sequence and the chromatin landscape in determining transcription factor binding intensity.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Acetylation Animals Binding Sites/genetics *Chromatin/genetics *DNA-Binding Proteins/genetics/metabolism Deoxyribonuclease I/genetics *Drosophila Proteins/genetics/metabolism *Drosophila melanogaster/genetics Gene Expression Regulation Genome, Insect Heat-Shock Response/genetics High-Throughput Nucleotide Sequencing Histones/genetics/metabolism Transcription Factors/*genetics/metabolism Transcriptional Activation/genetics |
| Subjects: | organism description > animal > insect > Drosophila bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Chromatin dynamics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > DNA binding protein bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > histone bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor |
| CSHL Authors: | |
| Communities: | CSHL labs > Siepel lab |
| Depositing User: | Matt Covey |
| Date: | 2012 |
| Date Deposited: | 15 Jan 2015 17:26 |
| Last Modified: | 15 Jan 2015 17:26 |
| PMCID: | PMC3315474 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31065 |
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