ArticleGenome research2006
Extensive low-affinity transcriptional interactions in the yeast genome.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
158 citing papers in PubMed, 258 citations in OpenAlex.
- The Semantics and Mechanisms of Enhancers and Promoters: "What Is True forAnnual review of biochemistry · 2026Review
- Unstructured transcription factor interactions enable emergent specificity.Science (New York, N.Y.) · 2026Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation.bioRxiv : the preprint server for biology · 2025Article
- IceQream: Quantitative chromosome accessibility analysis using physical TF models.Nature communications · 2025Article
- Article
- Collective unstructured interactions drive chromatin binding of transcription factors.bioRxiv : the preprint server for biology · 2025Article
- Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.Nature communications · 2025Article
- Modeling and designing enhancers by introducing and harnessing transcription factor binding units.Nature communications · 2025Article
- Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways.Nature communications · 2025Article
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- The nuance in DNA and transcription factor interactions.Nature reviews. Molecular cell biology · 2024Article
- KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.Scientific reports · 2023Article
- Cooperative assembly confers regulatory specificity and long-term genetic circuit stability.Cell · 2023Article
- DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.Nucleic acids research · 2023Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
- Deciphering the multi-scale, quantitative cis-regulatory code.Molecular cell · 2023Review
- Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.Nature biotechnology · 2022Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor-DNA interaction may therefore be important both evolutionarily and functionally.
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Registered trials
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.