Nature Genetics
36, 1331 - 1339 (2004)
Published online: 14 November 2004; | doi:10.1038/ng1473
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarraysSonali Mukherjee1, 2, 9, Michael F Berger1, 3, 9, Ghil Jona4, Xun S Wang1, 5, Dale Muzzey1, 3, Michael Snyder4, 6, Richard A Young5, 7
& Martha L Bulyk1, 2, 3, 81
Division of Genetics, Department of Medicine, Harvard Medical School; Boston; Massachusetts 02115; USA
2
Harvard/MIT Division of Health Sciences and Technology, Brigham and Women's Hospital and Harvard Medical School; Boston; Massachusetts 02115; USA
3
Harvard University Graduate Biophysics Program, Harvard Medical School; Boston; Massachusetts 02115; USA. 4
Departments of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA. 5
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. 6
Molecular Biophysics and Biochemistry, and Genetics, Yale University, New Haven, Connecticut 06520, USA. 7
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA. 8
Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA. 9
These authors contributed equally to this work.
Correspondence should be addressed to Martha L Bulyk mlbulyk@receptor.med.harvard.eduWe developed a new DNA microarray-based technology, called protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding−site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding−site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1. Comparison of these proteins' in vitro binding sites with their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames. Comparative sequence analysis indicated that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and, therefore, are probably functional in vivo binding sites that may be used in a condition-specific manner. Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes.
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