Nature Biotechnology
- 24, 1429 - 1435 (2006)
Published online: 24 September 2006; | doi:10.1038/nbt1246
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificitiesMichael F Berger1, 2, 7, Anthony A Philippakis1, 2, 3, 7, Aaron M Qureshi1, 4, Fangxue S He1, 3, Preston W Estep III5 & Martha L Bulyk1, 2, 3, 6, 1
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA. 2
Harvard University Graduate Biophysics Program, Cambridge, Massachusetts 02138, USA. 3
Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts 02115, USA. 4
Department of Mathematics, University of Maryland, College Park, Maryland 20742, USA. 5
Longenity, Inc., Waltham, Massachusetts 02451, USA. 6
Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA. 7
These authors contributed equally to this work.
Correspondence should be addressed to mlbulyk@receptor.med.harvard.edu Transcription factors (TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray (PBM) experiments1 that represents all possible DNA sequence variants of a given length k (that is, all 'k-mers') on a single, universal microarray. We constructed such all k-mer microarrays covering all 10–base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.
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