ArticleMolecular systems biology2017
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.
Article in Molecular systems biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- Identification and evaluation of 41 risk loci for juvenile idiopathic arthritis informs precision medicine: mechanistic implications of DNA topology and an HLA-A*02:01-ERAP2 interaction.medRxiv : the preprint server for health sciences · 2026Article
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- PROTAC-mediated regulation of programmed cell death: From molecular mechanisms to therapeutic breakthroughs.Innovation (Cambridge (Mass.)) · 2026Review
- Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction.NAR genomics and bioinformatics · 2026Article
- DNA breathing and shape encode distinct mechanisms of transcription factor binding.Bioinformatics advances · 2026Article
- TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction.Bioinformatics (Oxford, England) · 2025Article
- Predicting the DNA binding specificity of transcription factor mutants using family-level biophysically interpretable machine learning.Nucleic acids research · 2025Article
- Article
- Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing.Nucleic acids research · 2025Article
- Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD.bioRxiv : the preprint server for biology · 2024Article
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- A Study ofGenes · 2024Article
- Single-housing-induced islet epigenomic changes are related to polymorphisms in diabetic KK mice.Life science alliance · 2024Article
- RRM2 promotes the proliferation of chicken myoblasts, inhibits their differentiation and muscle regeneration.Poultry science · 2024Article
- Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.bioRxiv : the preprint server for biology · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.Biophysical journal · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.NAR genomics and bioinformatics · 2023Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Transcription factors (TFs) achieve DNA-binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT-SELEX experiments, the most extensive mammalian TF-DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif-flanking regions. Statistical machine-learning models combined with feature-selection techniques helped to reveal the nucleotide position-dependent DNA shape readout in TF-binding sites and the TF family-specific position dependence. Based on these results, we proposed novel DNA shape logos to visualize the DNA shape preferences of TFs. Overall, this work suggests a way of obtaining mechanistic insights into TF-DNA binding without relying on experimentally solved all-atom structures.
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