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

@article{citeulike:4240810, 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.}, author = {Hesselberth, Jay R. and Chen, Xiaoyu and Zhang, Zhihong and Sabo, Peter J. and Sandstrom, Richard and Reynolds, Alex P. and Thurman, Robert E. and Neph, Shane and Kuehn, Michael S. and Noble, William S. and Fields, Stanley and Stamatoyannopoulos, John A.}, citeulike-article-id = {4240810}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth.1313}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nmeth.1313}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19305407}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19305407}, day = {22}, doi = {10.1038/nmeth.1313}, issn = {1548-7105}, journal = {Nature methods}, keywords = {interaction, mapping}, month = {April}, number = {4}, pages = {283--289}, posted-at = {2009-04-15 18:20:37}, priority = {2}, publisher = {Nature Publishing Group}, title = {Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.}, url = {http://dx.doi.org/10.1038/nmeth.1313}, volume = {6}, year = {2009} }

TY - JOUR ID - citeulike:4240810 L3 - citeulike-article-id:4240810 N2 - 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. IS - 4 JF - Nature methods SN - 1548-7105 EP - 289 TI - Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. PB - Nature Publishing Group VL - 6 SP - 283 KW - interaction KW - mapping AU - Hesselberth, Jay AU - Chen, Xiaoyu AU - Zhang, Zhihong AU - Sabo, Peter AU - Sandstrom, Richard AU - Reynolds, Alex AU - Thurman, Robert AU - Neph, Shane AU - Kuehn, Michael AU - Noble, William AU - Fields, Stanley AU - Stamatoyannopoulos, John PY - 2009/04/22/ UR - http://dx.doi.org/10.1038/nmeth.1313 ER -