ArticleNature biotechnology2011
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.
Article in Nature biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
118 citing papers in PubMed.
- Article
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- Automated high-throughput selection of DNA aptamers using a common optical next-generation sequencer.Nucleic acids research · 2026Article
- Single-molecule parallel analysis for rapid exploration of sequence space.Nature protocols · 2026Review
- Multiplexed single-molecule characterization at the library scale.Nature protocols · 2026Review
- Article
- cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.PloS one · 2025Article
- Novel synthetic inducible promoters controlling gene expression during water-deficit stress with green tissue specificity in transgenic poplar.Plant biotechnology journal · 2024Article
- Regulatory activity is the default DNA state in eukaryotes.Nature structural & molecular biology · 2024Article
- Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening.Nature biomedical engineering · 2024Article
- Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability.RSC advances · 2024Article
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- High-throughput biochemistry in RNA sequence space: predicting structure and function.Nature reviews. Genetics · 2023Review
- Physicochemical models of protein-DNA binding with standard and modified base pairs.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Pooled genetic screens with image-based profiling.Molecular systems biology · 2022Review
- Massively Parallel Selection of NanoCluster Beacons.Advanced materials (Deerfield Beach, Fla.) · 2022Article
- Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq.Cell reports methods · 2022Article
- An open source toolkit for repurposing Illumina sequencing systems as versatile fluidics and imaging platforms.Scientific reports · 2022Article
- Navigating the pitfalls of applying machine learning in genomics.Nature reviews. Genetics · 2022Review
- Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization.International journal of molecular sciences · 2022Review
58 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Several methods for characterizing DNA-protein interactions are available, but none have demonstrated both high throughput and quantitative measurement of affinity. Here we describe 'high-throughput sequencing'-'fluorescent ligand interaction profiling' (HiTS-FLIP), a technique for measuring quantitative protein-DNA binding affinity at unprecedented depth. In this approach, the optics built into a high-throughput sequencer are used to visualize in vitro binding of a protein to sequenced DNA in a flow cell. Application of HiTS-FLIP to the protein Gcn4 (Gcn4p), the master regulator of the yeast amino acid starvation response, yielded ~440 million binding measurements, enabling determination of dissociation constants for all 12-mer sequences having submicromolar affinity. These data revealed a complex interdependency between motif positions, allowed improved discrimination of in vivo Gcn4p binding sites and regulatory targets relative to previous methods and showed that sets of genes with different promoter affinities to Gcn4p have distinct functions and expression kinetics. Broad application of this approach should increase understanding of the interactions that drive transcription.
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Registered trials
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