ArticlePloS one2017
A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 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.
The trial behind it
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
12 citing papers in PubMed, 19 citations in OpenAlex.
- Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models.Bioinformatics (Oxford, England) · 2025Article
- Emergence of activation or repression in transcriptional control under a fixed molecular context.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- Global repression by tailless during segmentation.Developmental biology · 2024Article
- Transcriptional activators in the early Drosophila embryo perform different kinetic roles.Cell systems · 2023Article
- A modERN resource: identification of Drosophila transcription factor candidate target genes using RNAi.Genetics · 2023Article
- Fully interpretable deep learning model of transcriptional control.Bioinformatics (Oxford, England) · 2020Article
- An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.PLoS computational biology · 2019Article
- The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages.PloS one · 2019Article
- Correction: A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.PloS one · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Metazoan gene expression is controlled through the action of long stretches of noncoding DNA that contain enhancers-shorter sequences responsible for controlling a single aspect of a gene's expression pattern. Models built on thermodynamics have shown how enhancers interpret protein concentration in order to determine specific levels of gene expression, but the emergent regulatory logic of a complete regulatory locus shows qualitative and quantitative differences from isolated enhancers. Such differences may arise from steric competition limiting the quantity of DNA that can simultaneously influence the transcription machinery. We incorporated this competition into a mechanistic model of gene regulation, generated efficient algorithms for this computation, and applied it to the regulation of Drosophila even-skipped (eve). This model finds the location of enhancers and identifies which factors control the boundaries of eve expression. This model predicts a new enhancer that, when assayed in vivo, drives expression in a non-eve pattern. Incorporation of chromatin accessibility eliminates this inconsistency.
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Identifiers
What OpenQuestion 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 OpenQuestion graph.