ArticleNature2007
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Article in Nature, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 353 papers, 1 of them a synthesis that pooled it.
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Who cites it
353 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Upstream open reading frames dynamically modulate CLOCK protein translation to regulate circadian rhythms and sleep.PLoS biology · 2025Article
- Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics.BMC genomics · 2025Article
- PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development.Life science alliance · 2024Article
- Multilevel omics for the discovery of biomarkers in pediatric sepsis.Pediatric investigation · 2023Review
- AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis.Genome biology and evolution · 2023Article
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- Identification of clade-wide putativeHorticulture research · 2023Article
- Systematic identification and characterization of repressive domains in Drosophila transcription factors.The EMBO journal · 2023Article
- circRNA432 enhances the coelomocyte phagocytosis via regulating the miR-2008-ELMO1 axis in Vibrio splendidus-challenged Apostichopus japonicus.Communications biology · 2023Article
- Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique.Frontiers in cellular and infection microbiology · 2023Article
- Spectrum of microRNAs and their target genes in cancer: intervention in diagnosis and therapy.Molecular biology reports · 2022Review
- BLSSpeller to discover novel regulatory motifs in maize.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Responses of different Drosophila species to temperature changes.The Journal of experimental biology · 2022Article
- Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans.Nature ecology & evolution · 2022Article
- Modular Evolution of the Drosophila Metabolome.Molecular biology and evolution · 2022Article
293 more citing papers are in PubMed but not listed here.
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46 authors.
Funding
Abstract
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.
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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.