期刊
NATURE BIOTECHNOLOGY
卷 24, 期 11, 页码 1429-1435出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt1246
关键词
-
资金
- NHGRI NIH HHS [R01 HG003985, R01 HG003420] Funding Source: Medline
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(1) 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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