ArticlePloS one2022
Transcription factor specificity limits the number of DNA-binding motifs.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Deep learning enabled prediction of nuclear lamina-associated chromatin.Patterns (New York, N.Y.) · 2026Article
- Article
- Decoding the role of DNA sequence on protein-DNA co-condensation.PLoS computational biology · 2025Article
- Harnessing p53 for targeted cancer therapy: new advances and future directions.Transcription · 2025Review
- Systematic discovery of DNA-binding tandem repeat proteins.Nucleic acids research · 2024Article
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Authors and funding
4 authors.
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Abstract
We study the limits imposed by transcription factor specificity on the maximum number of binding motifs that can coexist in a gene regulatory network, using the SwissRegulon Fantom5 collection of 684 human transcription factor binding sites as a model. We describe transcription factor specificity using regular expressions and find that most human transcription factor binding site motifs are separated in sequence space by one to three motif-discriminating positions. We apply theorems based on the pigeonhole principle to calculate the maximum number of transcription factors that can coexist given this degree of specificity, which is in the order of ten thousand and would fully utilize the space of DNA subsequences. Taking into account an expanded DNA alphabet with modified bases can further raise this limit by several orders of magnitude, at a lower level of sequence space usage. Our results may guide the design of transcription factors at both the molecular and system scale.
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