ArticleCell reports2017
Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.
Article in Cell reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- Locus-Scale Massively Parallel Reporter Assays.bioRxiv : the preprint server for biology · 2026Article
- From genes to patterns: a framework for modeling the emergence of embryonic development from transcriptional regulation.Frontiers in cell and developmental biology · 2025Article
- Mechanistic analysis of enhancer sequences in the estrogen receptor transcriptional program.Communications biology · 2024Article
- Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding.iScience · 2022Article
- Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks.Nucleic acids research · 2021Article
- Annotating the Insect Regulatory Genome.Insects · 2021Review
- Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo.Biophysical journal · 2019Article
- REDfly: the transcriptional regulatory element database for Drosophila.Nucleic acids research · 2019Article
- Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic.PLoS genetics · 2018Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Computational models of enhancer function generally assume that transcription factors (TFs) exert their regulatory effects independently, modeling an enhancer as a "bag of sites." These models fail on endogenous loci that harbor multiple enhancers, and a "two-tier" model appears better suited: in each enhancer TFs work independently, and the total expression is a weighted sum of their expression readouts. Here, we test these two opposing views on how cis-regulatory information is integrated. We fused two Drosophila blastoderm enhancers, measured their readouts, and applied the above two models to these data. The two-tier mechanism better fits these readouts, suggesting that these fused enhancers comprise multiple independent modules, despite having sequence characteristics typical of single enhancers. We show that short-range TF-TF interactions are not sufficient to designate such modules, suggesting unknown underlying mechanisms. Our results underscore that mechanisms of how modules are defined and how their outputs are combined remain to be elucidated.
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What Socratic holds
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 Socratic graph.