ArticleGenome research2002
Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 84 citations in OpenAlex.
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- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development.Development (Cambridge, England) · 2022Article
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- Transcriptional Enhancers inGenetics · 2020Review
- Systematic interrogation of human promoters.Genome research · 2019Article
- An Enhancer's Length and Composition Are Shaped by Its Regulatory Task.Frontiers in genetics · 2017Article
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- The grammar of transcriptional regulation.Human genetics · 2014Review
- Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome.BMC genomics · 2014Article
- Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.Chaos (Woodbury, N.Y.) · 2013Article
- Identification of thyroid hormone receptor binding sites in developing mouse cerebellum.BMC genomics · 2013Article
- A statistical thin-tail test of predicting regulatory regions in the Drosophila genome.Theoretical biology & medical modelling · 2013Article
- Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites.PLoS genetics · 2013Article
- Nucleosome-mediated cooperativity between transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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- Phylogeny disambiguates the evolution of heat-shock cis-regulatory elements in Drosophila.PloS one · 2010Article
- Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.Genome research · 2010Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 3 countries.
Funding
Abstract
The early developmental enhancers of Drosophila melanogaster comprise one of the most sophisticated regulatory systems in higher eukaryotes. An elaborate code in their DNA sequence translates both maternal and early embryonic regulatory signals into spatial distribution of transcription factors. One of the most striking features of this code is the redundancy of binding sites for these transcription factors (BSTF). Using this redundancy, we explored the possibility of predicting functional binding sites in a single enhancer region without any prior consensus/matrix description or evolutionary sequence comparisons. We developed a conceptually simple algorithm, Scanseq, that employs an original statistical evaluation for identifying the most redundant motifs and locates the position of potential BSTF in a given regulatory region. To estimate the biological relevance of our predictions, we built thorough literature-based annotations for the best-known Drosophila developmental enhancers and we generated detailed distribution maps for the most robust binding sites. The high statistical correlation between the location of BSTF in these experiment-based maps and the location predicted in silico by Scanseq confirmed the relevance of our approach. We also discuss the definition of true binding sites and the possible biological principles that govern patterning of regulatory regions and the distribution of transcriptional signals.
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