ArticleNature biotechnology2010
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis.
Article in Nature biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed, 191 citations in OpenAlex.
- Quantifying protein unfolding kinetics with a high-throughput microfluidic platform.Cell systems · 2026Article
- Amplicon/Protein Bead Display enables quantitativebioRxiv : the preprint server for biology · 2026Article
- Large field of view fluorescence imaging of microfluidic devices with a tandem-lens macroscope.Lab on a chip · 2026Article
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- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways.Nature communications · 2025Article
- High-throughput affinity measurements of direct interactions between activation domains and co-activators.bioRxiv : the preprint server for biology · 2024Article
- The method in the madness: Transcriptional control from stochastic action at the single-molecule scale.Current opinion in structural biology · 2024Review
- Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.Nature biomedical engineering · 2024Article
- Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases.Frontiers in bioscience (Scholar edition) · 2024Review
- Yeast transcription factor Msn2 binds to G4 DNA.Nucleic acids research · 2023Article
- KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.Scientific reports · 2023Article
- Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
- Microfluidic tool for rapid functional characterization of CRISPR complexes.New biotechnology · 2022Article
- High throughput and quantitative enzymology in the genomic era.Current opinion in structural biology · 2021Review
- Inferring primase-DNA specific recognition using a data driven approach.Nucleic acids research · 2021Article
- uPIC-M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry.ACS omega · 2021Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 6 institutions in 3 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.