ArticleNucleic acids research2017
Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- POU3F2 regulates canonical Wnt signalling via SOX13 and ADNP to expand the neural progenitor population.Brain : a journal of neurology · 2025Article
- An acidic residue within the OCT4 dimerization interface of SOX17 is necessary and sufficient to overcome its pluripotency-inducing activity.Stem cell reports · 2025Article
- Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominantGenome research · 2025Article
- The emergence of Sox and POU transcription factors predates the origins of animal stem cells.Nature communications · 2024Article
- TIANA: transcription factors cooperativity inference analysis with neural attention.BMC bioinformatics · 2024Article
- Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominantbioRxiv : the preprint server for biology · 2024Article
- A suboptimal OCT4-SOX2 binding site facilitates the naïve-state specific function of a Klf4 enhancer.PloS one · 2024Article
- Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX17.Nucleic acids research · 2023Article
- Clinical and Molecular Aspects Associated with Defects in the Transcription Factor POU3F4: A Review.Biomedicines · 2023Review
- The homeodomain of Oct4 is a dimeric binder of methylated CpG elements.Nucleic acids research · 2023Article
- Role of transcription factors and chromatin modifiers in driving lineage reprogramming in treatment-induced neuroendocrine prostate cancer.Frontiers in cell and developmental biology · 2023Review
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Biological importance of OCT transcription factors in reprogramming and development.Experimental & molecular medicine · 2021Review
- Genome wide identification, phylogeny, and synteny analysis ofBiotechnology reports (Amsterdam, Netherlands) · 2021Article
- The chromatin accessibility landscape reveals distinct transcriptional regulation in the induction of human primordial germ cell-like cells from pluripotent stem cells.Stem cell reports · 2021Article
- Research progress of the transcription factor Brn4 (Review).Molecular medicine reports · 2021Article
- Permissive epigenomes endow reprogramming competence to transcriptional regulators.Nature chemical biology · 2021Article
- Reprogramming competence of OCT factors is determined by transactivation domains.Science advances · 2020Article
- Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Article
- Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors.Cell reports · 2019Article
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9 authors.
Funding
Abstract
Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.
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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.