Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities Export

@article{citeulike:934384, abstract = {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.}, address = {[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] These authors contributed equally to this work.}, author = {Berger, Michael F. and Philippakis, Anthony A. and Qureshi, Aaron M. and He, Fangxue S. and Estep, Preston W. and Bulyk, Martha L.}, citeulike-article-id = {934384}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt1246}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt1246}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16998473}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16998473}, day = {24}, doi = {10.1038/nbt1246}, issn = {1087-0156}, journal = {Nature Biotechnology}, keywords = {msc}, month = {September}, number = {11}, pages = {1429--1435}, posted-at = {2006-11-21 06:33:25}, priority = {2}, publisher = {Nature Publishing Group}, title = {Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities}, url = {http://dx.doi.org/10.1038/nbt1246}, volume = {24}, year = {2006} }

TY - JOUR ID - citeulike:934384 L3 - citeulike-article-id:934384 N2 - 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. IS - 11 JF - Nature Biotechnology SN - 1087-0156 AD - [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] These authors contributed equally to this work. EP - 1435 TI - Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities PB - Nature Publishing Group VL - 24 SP - 1429 KW - msc AU - Berger, Michael AU - Philippakis, Anthony AU - Qureshi, Aaron AU - He, Fangxue AU - Estep, Preston AU - Bulyk, Martha PY - 2006/09/24/ UR - http://dx.doi.org/10.1038/nbt1246 ER -