De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-09

AUTHORS

Polly M Fordyce, Doron Gerber, Danh Tran, Jiashun Zheng, Hao Li, Joseph L DeRisi, Stephen R Quake

ABSTRACT

Gene expression is regulated in part by protein transcription factors that bind target regulatory DNA sequences. Predicting DNA binding sites and affinities from transcription factor sequence or structure is difficult; therefore, experimental data are required to link transcription factors to target sequences. We present a microfluidics-based approach for de novo discovery and quantitative biophysical characterization of DNA target sequences. We validated our technique by measuring sequence preferences for 28 Saccharomyces cerevisiae transcription factors with a variety of DNA-binding domains, including several that have proven difficult to study by other techniques. For each transcription factor, we measured relative binding affinities to oligonucleotides covering all possible 8-bp DNA sequences to create a comprehensive map of sequence preferences; for four transcription factors, we also determined absolute affinities. We expect that these data and future use of this technique will provide information essential for understanding transcription factor specificity, improving identification of regulatory sites and reconstructing regulatory interactions. More... »

PAGES

970

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt.1675

DOI

http://dx.doi.org/10.1038/nbt.1675

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1024784537

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/20802496


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