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

Nature biotechnology | Nov 9, 2006

http://www.ncbi.nlm.nih.gov/pubmed/16998473

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) experiments 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.

Pubmed ID: 16998473 RIS Download

Mesh terms: Animals | Basic Helix-Loop-Helix Leucine Zipper Transcription Factors | Binding Sites | Caenorhabditis elegans | Caenorhabditis elegans Proteins | Early Growth Response Protein 1 | Homeodomain Proteins | Humans | Mice | Octamer Transcription Factor-1 | Oligonucleotide Array Sequence Analysis | Protein Binding | Saccharomyces cerevisiae | Saccharomyces cerevisiae Proteins | Telomere-Binding Proteins | Transcription Factors

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