ArticleNature2011
A cis-regulatory map of the Drosophila genome.
Article in Nature, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 332 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.
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Who cites it
332 citing papers in PubMed, 537 citations in OpenAlex.
- Review
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- Transcriptional regulation of neuropeptide receptors underlies context-dependent adaptation in Drosophila melanogaster.FEBS open bio · 2026Article
- Cooperation between architectural C2H2 proteins in CP190 recruitment to Drosophila regulatory elements.Epigenetics & chromatin · 2025Article
- Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Functional genetic elements of a butterfly mimicry supergene.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.Nucleic acids research · 2025Article
- Epigenetic reprogramming induced by key metabolite depletion is an evolutionarily ancient path to tumorigenesis.Disease models & mechanisms · 2025Article
- Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis.Nature communications · 2025Article
- An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.PloS one · 2025Article
- Binding profiles for 961Genome research · 2024Article
- The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.Nucleic acids research · 2024Article
- New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity.Nucleic acids research · 2024Article
- A transcriptional enhancer regulates cardiac maturation.Nature cardiovascular research · 2024Article
- Clock-dependent chromatin accessibility rhythms regulate circadian transcription.PLoS genetics · 2024Article
- Organ transformation by environmental disruption of protein integrity and epigenetic memory in Drosophila.PLoS biology · 2024Article
- Article
- Polycomb protein binding and looping in the ON transcriptional state.Science advances · 2024Article
- Article
- Cis-regulatory polymorphism at fiz ecdysone oxidase contributes to polygenic evolutionary response to malnutrition in Drosophila.PLoS genetics · 2024Article
272 more citing papers are in PubMed but not listed here.
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Authors and funding
40 authors at 13 institutions in 3 countries.
Funding
Abstract
Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.
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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.