ArticleNucleic acids research2009
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 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
76 citing papers in PubMed.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- Biochemical principles of miRNA targeting in flies.Nature communications · 2026Article
- Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants.Research square · 2026Article
- Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review.Methods (San Diego, Calif.) · 2024Review
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays.Nucleic acids research · 2022Article
- Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.Nature biotechnology · 2022Article
- Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq.Cell reports methods · 2022Article
- Inferring primase-DNA specific recognition using a data driven approach.Nucleic acids research · 2021Article
- Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell reports methods · 2021Article
- DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq.Plant molecular biology · 2021Article
- Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement.Science advances · 2021Article
- Tools for experimental and computational analyses of off-target editing by programmable nucleases.Nature protocols · 2021Review
- Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression.Cell reports · 2020Article
- Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays.Nucleic acids research · 2020Article
- The Road Not Taken with Pyrrole-Imidazole Polyamides: Off-Target Effects and Genomic Binding.Biomolecules · 2020Review
- An improved bind-n-seq strategy to determine protein-DNA interactions validated using the bacterial transcriptional regulator YipR.BMC microbiology · 2020Article
- Updates on Aptamer Research.International journal of molecular sciences · 2019Review
- Adaptive Landscapes in the Age of Synthetic Biology.Molecular biology and evolution · 2019Review
- Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip.Molecular cell · 2019Article
16 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
3 authors.
Funding
Abstract
Transcription factor-DNA interactions are some of the most important processes in biology because they directly control hereditary information. The targets of most transcription factor are unknown. In this report, we introduce Bind-n-Seq, a new high-throughput method for analyzing protein-DNA interactions in vitro, with several advantages over current methods. The procedure has three steps (i) binding proteins to randomized oligonucleotide DNA targets, (ii) sequencing the bound oligonucleotide with massively parallel technology and (iii) finding motifs among the sequences. De novo binding motifs determined by this method for the DNA-binding domains of two well-characterized zinc-finger proteins were similar to those described previously. Furthermore, calculations of the relative affinity of the proteins for specific DNA sequences correlated significantly with previous studies (R(2 )= 0.9). These results present Bind-n-Seq as a highly rapid and parallel method for determining in vitro binding sites and relative affinities.
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Registered trials
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