ArticleMolecular and cellular biology2005
cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster.
Article in Molecular and cellular biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 74 citations in OpenAlex.
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- Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.Mathematical biosciences · 2021Article
- Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks.Nucleic acids research · 2021Article
- A Mutation in theG3 (Bethesda, Md.) · 2020Article
- Seven myths of how transcription factors read the cis-regulatory code.Current opinion in systems biology · 2020Article
- The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages.PloS one · 2019Article
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- Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation.BMC systems biology · 2017Article
- Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.Cell reports · 2017Article
- Drosophila poised enhancers are generated during tissue patterning with the help of repression.Genome research · 2017Article
- Article
- The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification.Developmental biology · 2016Article
- Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression.Nature communications · 2016Article
- Suboptimization of developmental enhancers.Science (New York, N.Y.) · 2015Article
- Analysis of functional importance of binding sites in the Drosophila gap gene network model.BMC genomics · 2015Article
- A gene-specific non-enhancer sequence is critical for expression from the promoter of the small heat shock protein gene αB-crystallin.Human genomics · 2014Article
- Sequence-based model of gap gene regulatory network.BMC genomics · 2014Article
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2 authors at 1 institution in 1 country.
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Abstract
Bioinformatics analysis of transcriptional control is guided by knowledge of the characteristics of cis-regulatory regions or enhancers. Features such as clustering of binding sites and co-occurrence of binding sites have aided enhancer identification, but quantitative predictions of enhancer function are not yet generally feasible. To facilitate the analysis of regulatory sequences in Drosophila melanogaster, we identified quantitative parameters that affect the activity of short-range transcriptional repressors, proteins that play key roles in development. In addition to the previously noted distance dependence, repression is strongly influenced by the stoichiometry, affinity, spacing, and arrangement of activator binding sites. Repression is insensitive to the type of activation domain, suggesting that short-range repression may primarily affect activators at the level of DNA binding. The activity of several short-range, but not long-range, repressors is circumscribed by the same quantitative parameters. This cis-regulatory "grammar" may aid the identification of enhancers regulated by short-range repressors and facilitate bioinformatic prediction of the functional output of transcriptional regulatory sequences.
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