ArticleNature biotechnology2006
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Article in Nature biotechnology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 430 papers.
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Who cites it
430 citing papers in PubMed, 714 citations in OpenAlex.
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- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- NPBIP: predicting binding preferences of uncharacterized nucleic-acid-binding proteins.Bioinformatics (Oxford, England) · 2026Article
- BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.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
- PoolParty: streamlined design of DNA sequence libraries in Python.bioRxiv : the preprint server for biology · 2026Article
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- 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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- Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression.NPJ systems biology and applications · 2026Article
- DNA methylation shapes transcription factor binding beyond canonical CpG contexts.Proceedings of the National Academy of Sciences of the United States of America · 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
- 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
370 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Transcription factors (TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray (PBM) experiments that represents all possible DNA sequence variants of a given length k (that is, all 'k-mers') on a single, universal microarray. We constructed such all k-mer microarrays covering all 10-base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.
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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.