ArticleGenome research2016
Interactions between pluripotency factors specify cis-regulation in embryonic stem cells.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 58 citations in OpenAlex.
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- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
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- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- A suboptimal OCT4-SOX2 binding site facilitates the naïve-state specific function of a Klf4 enhancer.PloS one · 2024Article
- Transcription factor interactions explain the context-dependent activity of CRX binding sites.PLoS computational biology · 2024Article
- Review
- Nuclear Factor Kappa B Promotes Ferritin Heavy Chain Expression inInternational journal of molecular sciences · 2022Article
- Repetitive DNA symmetry elements negatively regulate gene expression in embryonic stem cells.Biophysical journal · 2022Article
- DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.Nature genetics · 2022Article
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- A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells.Genome research · 2021Article
- Enhancer grammar in development, evolution, and disease: dependencies and interplay.Developmental cell · 2021Review
- Base-resolution models of transcription-factor binding reveal soft motif syntax.Nature genetics · 2021Article
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.Nature communications · 2021Article
- Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts.Biological psychiatry · 2021Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We investigated how interactions between pluripotency transcription factors (TFs) affect cis-regulation. We created hundreds of synthetic cis-regulatory elements (CREs) comprised of combinations of binding sites for pluripotency TFs and measured their expression in mouse embryonic stem (ES) cells. A thermodynamic model that incorporates interactions between TFs explains a large portion (72%) of the variance in expression of these CREs. These interactions include three favorable heterotypic interactions between TFs. The model also predicts an unfavorable homotypic interaction between TFs, helping to explain the observation that homotypic chains of binding sites express at low levels. We further investigated the expression driven by CREs comprised of homotypic chains of KLF4 binding sites. Our results suggest that KLF homologs make unique contributions to regulation by these CREs. We conclude that a specific set of interactions between pluripotency TFs plays a large role in setting the levels of expression driven by CREs in ES cells.
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