ArticleGenome research2015
A widespread role of the motif environment in transcription factor binding across diverse protein families.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- RegRegSEA: a web server for regulatory region set enrichment analysis of epigenomic data.Nucleic acids research · 2026Article
- Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors.NAR genomics and bioinformatics · 2026Article
- Article
- Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor.Nature communications · 2025Article
- Paused RNA polymerase primes promoters via RNA-mediated stabilisation of transcription factor ERα.Nature communications · 2025Article
- Combining Motifs, CRE Activity, And Gene Expression Data Using ML Greatly Improves the Accuracy of Tissue-Specific TF Network Maps.bioRxiv : the preprint server for biology · 2025Article
- Article
- Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.Genome research · 2025Article
- PhWRKY30 activates salicylic acid biosynthesis to positively regulate antiviral defense response in petunia.Horticulture research · 2025Article
- Modeling and designing enhancers by introducing and harnessing transcription factor binding units.Nature communications · 2025Article
- Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST.PloS one · 2025Article
- TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors.Genome biology · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences.FEBS letters · 2024Article
- PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.BMC bioinformatics · 2023Article
- Emerging insights into enhancer biology and function.Transcription · 2023Review
- Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs.bioRxiv : the preprint server for biology · 2023Article
- Deep flanking sequence engineering for efficient promoter design using DeepSEED.Nature communications · 2023Article
- Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box DNA motifs.Scientific reports · 2023Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regions. Interestingly, based on a vast amount of data accumulated from genomic assays, it has been shown that only a small fraction of all potential binding sites containing the consensus motif of a given TF actually bind the protein. Recent in vitro binding assays, which exclude the effects of the cellular environment, also demonstrate selective TF binding. An intriguing conjecture is that the surroundings of cognate binding sites have unique characteristics that distinguish them from other sequences containing a similar motif that are not bound by the TF. To test this hypothesis, we conducted a comprehensive analysis of the sequence and DNA shape features surrounding the core-binding sites of 239 and 56 TFs extracted from in vitro HT-SELEX binding assays and in vivo ChIP-seq data, respectively. Comparing the nucleotide content of the regions around the TF-bound sites to the counterpart unbound regions containing the same consensus motifs revealed significant differences that extend far beyond the core-binding site. Specifically, the environment of the bound motifs demonstrated unique sequence compositions, DNA shape features, and overall high similarity to the core-binding motif. Notably, the regions around the binding sites of TFs that belong to the same TF families exhibited similar features, with high agreement between the in vitro and in vivo data sets. We propose that these unique features assist in guiding TFs to their cognate binding sites.
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