ArticleNucleic acids research2016
Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 21 citations in OpenAlex.
- Dual regulation of transcription factor binding by tup11/12-mediated destabilization and DNA loop-mediated stabilization ensures stress-specific gene activation in fission yeast.Nucleic acids research · 2026Article
- Versatile Microfluidics Platform for Enhanced Multitarget Super-Resolution Microscopy.ACS nano · 2026Article
- Multi-faceted regulation of CREB family transcription factors.Frontiers in molecular neuroscience · 2024Review
- Affinity microfluidics enables high-throughput protein degradation analysis in cell-free extracts.Communications biology · 2022Article
- Alternative Splicing Isoforms of PorcineGenes · 2022Article
- Microfluidic tool for rapid functional characterization of CRISPR complexes.New biotechnology · 2022Article
- What turns CREB on? And off? And why does it matter?Cellular and molecular life sciences : CMLS · 2020Review
- Targeting DNA binding proteins for cancer therapy.Cancer science · 2020Review
- Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy.International journal of molecular sciences · 2020Review
- SIRT6 Promotes Hepatic Beta-Oxidation via Activation of PPARα.Cell reports · 2019Article
- Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions.Nucleic acids research · 2019Article
- Microfluidic epigenomic mapping technologies for precision medicine.Lab on a chip · 2019Review
- Exclusive Temporal Stimulation of IL-10 Expression in LPS-Stimulated Mouse Macrophages by cAMP Inducers and Type I Interferons.Frontiers in immunology · 2019Article
- A high-throughput integrated microfluidics method enables tyrosine autophosphorylation discovery.Communications biology · 2019Article
- Modeling protein-DNA binding via high-throughput in vitro technologies.Briefings in functional genomics · 2017Article
- Microfluidics for genome-wide studies involving next generation sequencing.Biomicrofluidics · 2017Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein binding to DNA is a fundamental process in gene regulation. Methodologies such as ChIP-Seq and mapping of DNase I hypersensitive sites provide global information on this regulation in vivo In vitro methodologies provide valuable complementary information on protein-DNA specificities. However, current methods still do not measure absolute binding affinities. There is a real need for large-scale quantitative protein-DNA affinity measurements. We developed QPID, a microfluidic application for measuring protein-DNA affinities. A single run is equivalent to 4096 gel-shift experiments. Using QPID, we characterized the different affinities of ATF1, c-Jun, c-Fos and AP-1 to the CRE consensus motif and CRE half-site in two different genomic sequences on a single device. We discovered that binding of ATF1, but not of AP-1, to the CRE half-site is highly affected by its genomic context. This effect was highly correlated with ATF1 ChIP-seq and PBM experiments. Next, we characterized the affinities of ATF1 and ATF3 to 128 genomic CRE and CRE half-site sequences. Our affinity measurements explained that in vivo binding differences between ATF1 and ATF3 to CRE and CRE half-sites are partially mediated by differences in the minor groove width. We believe that QPID would become a central tool for quantitative characterization of biophysical aspects affecting protein-DNA binding.
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