ArticleeLife2022
Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed, 24 citations in OpenAlex.
- DynamicAtlas: a morphodynamic atlas for Drosophila development.Nature methods · 2026Article
- Article
- Collective unstructured interactions drive chromatin binding of transcription factors.bioRxiv : the preprint server for biology · 2025Article
- Active learning of enhancers and silencers in the developing neural retina.Cell systems · 2025Article
- Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development.Genetics · 2025Article
- From genes to patterns: a framework for modeling the emergence of embryonic development from transcriptional regulation.Frontiers in cell and developmental biology · 2025Article
- Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns.PLoS computational biology · 2024Article
- Optogenetic dissection of transcriptional repression in a multicellular organism.Nature communications · 2024Article
- Plant enhancers exhibit both cooperative and additive interactions among their functional elements.The Plant cell · 2024Article
- Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in earlyeLife · 2023Article
- Post-transcriptional checkpoints in autoimmunity.Nature reviews. Rheumatology · 2023Review
- A bistable autoregulatory module in the developing embryo commits cells to binary expression fates.Current biology : CB · 2023Article
- Competing constraints shape the nonequilibrium limits of cellular decision-making.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- Notch-dependent and -independent transcription are modulated by tissue movements at gastrulation.eLife · 2022Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit fly embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity captures the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.
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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.