"Global mapping of protein-DNA interactions in vivo by digital genomic footprinting"

Jay R. Hesselberth, Xiaoyu Chen, Zhihong Zhang, Peter J. Sabo, Richard Sandstrom, Alex P. Reynolds, Robert E. Thurman, Shane Neph, Michael S. Kuehn, William S. Noble, Stanley Fields and John A. Stamatoyannopoulos

Nature Methods. 6(4):283-289, 2009.


The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of eukaryotic genomes. We developed a digital approach to assay regulatory protein occupancy on genomic DNA in vivo by dense mapping of individual DNase I cleavages from intact nuclei using massively parallel DNA sequencing. Analysis of >23 million cleavages across the Saccharomyces cerevisiae genome revealed thousands of protected regulatory protein footprints, enabling de novo derivation of factor binding motifs as well as the identification of hundreds of novel binding sites for major regulators. We observed striking correspondence between nucleotide-level DNase I cleavage patterns and protein-DNA interactions determined by crystallography. The data also yielded a detailed view of larger chromatin features including positioned nucleosomes flanking factor binding regions. Digital genomic footprinting provides a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence.

Data files

Source code

The shell script footprinting_run_all.sh takes as input the tag counts, the mappability data and the locations of yeast intergenic regions, and produces as output a list of footprints with associated q-values. The script calls three other scripts, which are listed below. To run the scripts, you must have Python and Matlab installed on your system.

The footprints file was created using the following command line:

      footprinting_run_all.sh yeast.dnaseI.tagCounts.bed yeast.unmappableBase.bed yeast.intergenic.bed yeast.footprints.bed

Nature Methods