Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-11

AUTHORS

Michael F Berger, Anthony A Philippakis, Aaron M Qureshi, Fangxue S He, Preston W Estep, Martha L Bulyk

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) 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. More... »

PAGES

1429-1435

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt1246

DOI

http://dx.doi.org/10.1038/nbt1246

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1046227460

PUBMED

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


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