ArticleNucleic acids research2014
Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 57 citations in OpenAlex.
- Mechanisms of gene regulation by SRCAP and H2A.Z.Nature communications · 2026Article
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- Geometric deep learning of protein-DNA binding specificity.Nature methods · 2024Article
- The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.Nucleic acids research · 2024Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
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- Specifically bound BZIP transcription factors modulate DNA supercoiling transitions.Scientific reports · 2020Article
- Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro.Nucleic acids research · 2019Article
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- Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.eLife · 2018Article
- Local sequence features that influence AP-1Genome research · 2018Article
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- Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States.Biochemistry · 2017Article
- DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.Bioinformatics (Oxford, England) · 2017Article
- Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.Biochemistry · 2017Article
- DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2017Article
- Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.Scientific reports · 2017Article
- A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells.Nucleic acids research · 2017Article
- Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.Molecular systems biology · 2017Article
- How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Protein-DNA recognition is a critical component of gene regulatory processes but the underlying molecular mechanisms are not yet completely understood. Whereas the DNA binding preferences of transcription factors (TFs) are commonly described using nucleotide sequences, the 3D DNA structure is recognized by proteins and is crucial for achieving binding specificity. However, the ability to analyze DNA shape in a high-throughput manner made it only recently feasible to integrate structural information into studies of protein-DNA binding. Here we focused on the homeodomain family of TFs and analyzed the DNA shape of thousands of their DNA binding sites, investigating the covariation between the protein sequence and the sequence and shape of their DNA targets. We found distinct homeodomain regions that were more correlated with either the nucleotide sequence or the DNA shape of their preferred binding sites, demonstrating different readout mechanisms through which homeodomains attain DNA binding specificity. We identified specific homeodomain residues that likely play key roles in DNA recognition via shape readout. Finally, we showed that adding DNA shape information when characterizing binding sites improved the prediction accuracy of homeodomain binding specificities. Taken together, our findings indicate that DNA shape information can generally provide new mechanistic insights into TF binding.
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