ArticleCell reports2013
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
Article in Cell reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 227 papers.
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Who cites it
227 citing papers in PubMed.
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- Cis- and trans-regulatory factors contributing to divergent activity of the TDH3 promoter in Saccharomyces yeast.Molecular biology and evolution · 2026Article
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Independent component analysis deciphers the genetic basis of cotton fiber elongation through eQTLs and sQTLs.Journal of advanced research · 2026Article
- Mapping DNA glycosylase binding across lesion sequence contexts reveals extended sequence and structural recognition logic.Nature communications · 2026Article
- PoolParty: streamlined design of DNA sequence libraries in Python.bioRxiv : the preprint server for biology · 2026Article
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- Multimodal bHLH-PAS DNA binding controls specificity and drives obesity.Nucleic acids research · 2026Article
- DNA breathing and shape encode distinct mechanisms of transcription factor binding.Bioinformatics advances · 2026Article
- TF paralogs-Natural experiments in DNA binding.Current opinion in structural biology · 2025Review
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- Cistromic insight into the association of retinoid X receptor with MyoD and CTCF in proliferating myoblasts.Scientific reports · 2025Article
- Article
167 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein-binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. Using yeast TFs Cbf1 and Tye7 as our case studies, we found that binding sites of these bHLH TFs (i.e., E-boxes) are bound differently in vitro and in vivo, depending on their genomic context. Computational analyses suggest that nucleotides outside E-box binding sites contribute to specificity by influencing the three-dimensional structure of DNA binding sites. Thus, the local shape of target sites might play a widespread role in achieving regulatory specificity within TF families.
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