ArticleNature2014
Genome-scale functional characterization of Drosophila developmental enhancers in vivo.
Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 277 papers.
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Who cites it
277 citing papers in PubMed, 510 citations in OpenAlex.
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Chromosomal inversions modulate 3D chromatin interactions and regulatory architecture inResearch square · 2026Article
- Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse.bioRxiv : the preprint server for biology · 2026Article
- NovelbioRxiv : the preprint server for biology · 2026Article
- Tuning mitotic recombination with patterned DNA nicks for precision mosaic analysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Enhancer placement impacts transcriptional dynamics in Drosophila embryos.Nature communications · 2026Article
- A genome-wide survey reveals that a diverse array of enhancers coordinates theGenome research · 2026Article
- Article
- Article
- Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling.Nature communications · 2026Article
- 3D chromatin structures precede genome activation in Drosophila embryogenesis.Cell genomics · 2025Article
- Neural control of coordinated wing and leg movements during a terrestrial threat display.bioRxiv : the preprint server for biology · 2025Article
- A genome-wide survey reveals a diverse array of enhancers coordinate thebioRxiv : the preprint server for biology · 2025Article
- Uncovering hidden enhancers through unbiased in vivo testing.Nature communications · 2025Article
- Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.Nucleic acids research · 2025Article
- Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.iScience · 2025Article
- Spatial constraints and cell surface molecule depletion structure a randomly connected learning circuit.Current biology : CB · 2025Article
217 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional enhancers are crucial regulators of gene expression and animal development and the characterization of their genomic organization, spatiotemporal activities and sequence properties is a key goal in modern biology. Here we characterize the in vivo activity of 7,705 Drosophila melanogaster enhancer candidates covering 13.5% of the non-coding non-repetitive genome throughout embryogenesis. 3,557 (46%) candidates are active, suggesting a high density with 50,000 to 100,000 developmental enhancers genome-wide. The vast majority of enhancers display specific spatial patterns that are highly dynamic during development. Most appear to regulate their neighbouring genes, suggesting that the cis-regulatory genome is organized locally into domains, which are supported by chromosomal domains, insulator binding and genome evolution. However, 12 to 21 per cent of enhancers appear to skip non-expressed neighbours and regulate a more distal gene. Finally, we computationally identify cis-regulatory motifs that are predictive and required for enhancer activity, as we validate experimentally. This work provides global insights into the organization of an animal regulatory genome and the make-up of enhancer sequences and confirms and generalizes principles from previous studies. All enhancer patterns are annotated manually with a controlled vocabulary and all results are available through a web interface (http://enhancers.starklab.org), including the raw images of all microscopy slides for manual inspection at arbitrary zoom levels.
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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.