ArticleGenome research2011
Combinatorial binding of transcription factors in the pluripotency control regions of the genome.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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.
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Who cites it
20 citing papers in PubMed, 40 citations in OpenAlex.
- Article
- Jade1 and the HBO1 histone acetyltransferase complex are spatial-selective cofactors of the pluripotency transcription factor Oct4.The Journal of biological chemistry · 2025Article
- Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.Developmental cell · 2025Article
- Transcriptional co-regulator OCA-B/Pou2af1 restricts Th2 differentiation.Frontiers in immunology · 2025Article
- Oct4 redox sensitivity potentiates reprogramming and differentiation.Genes & development · 2024Article
- A Random Forest-Based Genome-Wide Scan Reveals Fertility-Related Candidate Genes and Potential Inter-Chromosomal Epistatic Regions Associated With Age at First Calving in Nellore Cattle.Frontiers in genetics · 2022Article
- Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming.Cellular and molecular life sciences : CMLS · 2018Review
- HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region.American journal of human genetics · 2016Article
- The Oct1 transcription factor and epithelial malignancies: Old protein learns new tricks.Biochimica et biophysica acta · 2016Review
- Functional interplay between the RK motif and linker segment dictates Oct4-DNA recognition.Nucleic acids research · 2015Article
- Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion.Molecular and cellular biology · 2015Article
- Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome.Molecular bioSystems · 2015Article
- Article
- Protein-DNA binding: complexities and multi-protein codes.Nucleic acids research · 2014Review
- Oct transcription factors in development and stem cells: insights and mechanisms.Development (Cambridge, England) · 2013Review
- Endogenous retrovirus-K promoter: a landing strip for inflammatory transcription factors?Retrovirology · 2013Review
- SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state.PLoS genetics · 2013Article
- Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.PloS one · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The pluripotency control regions (PluCRs) are defined as genomic regions that are bound by POU5F1, SOX2, and NANOG in vivo. We utilized a high-throughput binding assay to record more than 270,000 different DNA/protein binding measurements along incrementally tiled windows of DNA within these PluCRs. This high-resolution binding map is then used to systematically define the context of POU factor binding, and reveals patterns of cooperativity and competition in the pluripotency network. The most prominent pattern is a pervasive binding competition between POU5F1 and the forkhead transcription factors. Like many transcription factors, POU5F1 is co-expressed with a paralog, POU2F1, that shares an apparently identical binding specificity. By analyzing thousands of binding measurements, we discover context effects that discriminate POU2F1 from POU5F1 binding. Proximal NANOG binding promotes POU5F1 binding, whereas nearby SOX2 binding favors POU2F1. We demonstrate by cross-species comparison and by chromatin immunoprecipitation (ChIP) that the contextual sequence determinants learned in vitro are sufficient to predict POU2F1 binding 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.