ArticleNucleic acids research2009
Organization of developmental enhancers in the Drosophila embryo.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 56 citations in OpenAlex.
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Global repression by tailless during segmentation.Developmental biology · 2024Article
- Increased chromatin accessibility promotes the evolution of a transcriptional silencer inScience advances · 2023Article
- Review
- Modulating the bicoid gradient in space and time.Hereditas · 2021Article
- Annotating the Insect Regulatory Genome.Insects · 2021Review
- Enhancer grammar in development, evolution, and disease: dependencies and interplay.Developmental cell · 2021Review
- Base-resolution models of transcription-factor binding reveal soft motif syntax.Nature genetics · 2021Article
- Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation.Genome research · 2019Article
- An Enhancer's Length and Composition Are Shaped by Its Regulatory Task.Frontiers in genetics · 2017Article
- Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.PLoS genetics · 2015Article
- A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes.PloS one · 2015Article
- In pursuit of design principles of regulatory sequences.Nature reviews. Genetics · 2014Review
- CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.Nucleic acids research · 2014Article
- Article
- Simulations of enhancer evolution provide mechanistic insights into gene regulation.Molecular biology and evolution · 2014Article
- Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.Nucleic acids research · 2013Article
- Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.Genome biology · 2013Article
- Article
- Deep sequencing and expression of microRNAs from early honeybee (Apis mellifera) embryos reveals a role in regulating early embryonic patterning.BMC evolutionary biology · 2012Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Most cell-specific enhancers are thought to lack an inherent organization, with critical binding sites distributed in a more or less random fashion. However, there are examples of fixed arrangements of binding sites, such as helical phasing, that promote the formation of higher-order protein complexes on the enhancer DNA template. Here, we investigate the regulatory 'grammar' of nearly 100 characterized enhancers for developmental control genes active in the early Drosophila embryo. The conservation of grammar is examined in seven divergent Drosophila genomes. Linked binding sites are observed for particular combinations of binding motifs, including Bicoid-Bicoid, Hunchback-Hunchback, Bicoid-Dorsal, Bicoid-Caudal and Dorsal-Twist. Direct evidence is presented for the importance of Bicoid-Dorsal linkage in the integration of the anterior-posterior and dorsal-ventral patterning systems. Hunchback-Hunchback interactions help explain unresolved aspects of segmentation, including the differential regulation of the eve stripe 3 + 7 and stripe 4 + 6 enhancers. We also present evidence that there is an under-representation of nucleosome positioning sequences in many enhancers, raising the possibility for a subtle higher-order structure extending across certain enhancers. We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo.
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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.