ArticleNature protocols2009
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.
Article in Nature protocols, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 243 papers.
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Who cites it
243 citing papers in PubMed.
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- Mapping DNA glycosylase binding across lesion sequence contexts reveals extended sequence and structural recognition logic.Nature communications · 2026Article
- Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.bioRxiv : the preprint server for biology · 2026Article
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Defining the DNA Binding Specificity of GRHL2.bioRxiv : the preprint server for biology · 2026Article
- A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male development.Nature communications · 2026Article
- Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals.bioRxiv : the preprint server for biology · 2026Article
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- How negative sampling shapes the performance of transcription factor binding site prediction models.Bioinformatics (Oxford, England) · 2026Article
- A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFold 3.Nucleic acids research · 2026Article
- Overexpression of Tempranillo-Like Proteins Promotes Dormancy Release in Poplar.Plant, cell & environment · 2025Article
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity.Cell reports · 2025Article
- Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus.Nature communications · 2025Article
- Chemical Engineering of Transcription Factors Uncovered Cell-Permeable μMax Modulators.Journal of the American Chemical Society · 2025Article
- Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.Communications biology · 2025Article
183 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Protein-binding microarray (PBM) technology provides a rapid, high-throughput means of characterizing the in vitro DNA-binding specificities of transcription factors (TFs). Using high-density, custom-designed microarrays containing all 10-mer sequence variants, one can obtain comprehensive binding-site measurements for any TF, regardless of its structural class or species of origin. Here, we present a protocol for the examination and analysis of TF-binding specificities at high resolution using such 'all 10-mer' universal PBMs. This procedure involves double-stranding a commercially synthesized DNA oligonucleotide array, binding a TF directly to the double-stranded DNA microarray and labeling the protein-bound microarray with a fluorophore-conjugated antibody. We describe how to computationally extract the relative binding preferences of the examined TF for all possible contiguous and gapped 8-mers over the full range of affinities, from highest affinity sites to nonspecific sites. Multiple proteins can be tested in parallel in separate chambers on a single microarray, enabling the processing of a dozen or more TFs in a single day.
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