Global Mapping of Protein-DNA Interactions in Vivo by Digital Genomic Footprinting

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2009 Mar 24

PMID 19305407

Citations 360

Authors

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

John A Stamatoyannopoulos

Affiliations

Soon will be listed here.

Abstract

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 and the identification of hundreds of new binding sites for major regulators. We observed striking correspondence between single-nucleotide resolution 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 should be a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence.

Citing Articles

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