ArticleCell2011
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Article in Cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 317 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
317 citing papers in PubMed, 533 citations in OpenAlex.
- A transcription factor by any other name - function beyond DNA binding and transactivation.EMBO reports · 2026Review
- A transcription factor regulates development of a bacteria-housing eukaryotic cell through DNA damage mitigation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Decoding the mechanisms of cooperative DNA binding by the Paired-like homeodomain family.Nature communications · 2026Article
- Liquid-Liquid Phase Separation (LLPS) in Tumor Biology: Special Focus on the Process of Transcription.International journal of molecular sciences · 2026Review
- Review
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors.NAR genomics and bioinformatics · 2026Article
- HOXB4 Promotes Bladder Cancer Progression in Part Through Transcriptional Activation of Smoothened.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- Multimodal bHLH-PAS DNA binding controls specificity and drives obesity.Nucleic acids research · 2026Article
- PBX-dependent and independent Hox programs establish and maintain motor neuron terminal Identity.bioRxiv : the preprint server for biology · 2025Article
- AP1 is a pioneer transcription factor that programmes cell fate through MADS-domain protein tetramerisation.Genome biology · 2025Article
- HOXA5-driven transcriptional program in lung development.Developmental biology · 2025Article
- DNA bendability regulates transcription factor binding to nucleosomes.Nature structural & molecular biology · 2025Article
- TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction.Bioinformatics (Oxford, England) · 2025Article
- Decoding the mechanisms of cooperative DNA binding by the Paired-like homeodomain family.bioRxiv : the preprint server for biology · 2025Article
- Article
- Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
257 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.
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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.