ArticleNucleic acids research2015
DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 42 citations in OpenAlex.
- A robust cis-regulatory network ensures Otx2 expression during retinal development.Development (Cambridge, England) · 2026Article
- Molecular Cloning, Optimization of Expression and Functional Characterization of the Global Transcriptional Regulator MosR (Rv0348) of Mycobacterium tuberculosis.Applied biochemistry and biotechnology · 2025Article
- The emergence of Sox and POU transcription factors predates the origins of animal stem cells.Nature communications · 2024Article
- Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants.Molecular systems biology · 2024Article
- Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology.Cell systems · 2023Article
- Improving cooperativity of transcription activators by oligomerization domains in mammalian cells.Synthetic and systems biotechnology · 2023Article
- The homeodomain of Oct4 is a dimeric binder of methylated CpG elements.Nucleic acids research · 2023Article
- Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.Journal of integrative bioinformatics · 2021Article
- Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.Nature communications · 2020Article
- OCT4 and PAX6 determine the dual function of SOX2 in human ESCs as a key pluripotent or neural factor.Stem cell research & therapy · 2019Article
- Allosterism and signal transfer in DNA.Nucleic acids research · 2018Article
- DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.Nucleic acids research · 2018Article
- Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming.Cellular and molecular life sciences : CMLS · 2018Review
- Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea.Developmental biology · 2018Article
- Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization.PloS one · 2018Article
- Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.Nucleic acids research · 2017Article
- Examining cooperative binding of Sox2 on DC5 regulatory element upon complex formation with Pax6 through excess electron transfer assay.Nucleic acids research · 2016Article
- Mechanisms of Specificity for Hox Factor Activity.Journal of developmental biology · 2016Article
- Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction.Nucleic acids research · 2016Article
- Glucose-dependent downregulation of glucagon gene expression mediated by selective interactions between ALX3 and PAX6 in mouse alpha cells.Diabetologia · 2016Article
Corrections and comments
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Authors and funding
10 authors at 7 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.
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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.