ArticleDevelopmental dynamics : an official publication of the American Association of Anatomists2012
Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.
Article in Developmental dynamics : an official publication of the American Association of Anatomists, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 23 citations in OpenAlex.
- The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.Biology open · 2025Article
- scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development.Developmental cell · 2024Article
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- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- Mutational analysis of a Drosophila neuroblast enhancer governing nubbin expression during CNS development.Genesis (New York, N.Y. : 2000) · 2018Article
- Article
- Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.Genome biology and evolution · 2018Article
- Genes implicated in stem cell identity and temporal programme are directly targeted by Notch in neuroblast tumours.Development (Cambridge, England) · 2016Article
- cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers.BMC genomics · 2015Article
- Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.Nucleic acids research · 2014Article
- Article
- Transcription factors: from enhancer binding to developmental control.Nature reviews. Genetics · 2012Review
- i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.Nucleic acids research · 2012Article
- Unique alterations of an ultraconserved non-coding element in the 3'UTR of ZIC2 in holoprosencephaly.PloS one · 2012Article
- The cis-regulatory dynamics of the Drosophila CNS determinant castor are controlled by multiple sub-pattern enhancers.Gene expression patterns : GEPArticle
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11 authors at 5 institutions in 1 country.
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Abstract
backgroundPhylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs.
resultsWe have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization.
conclusionscis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process.
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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.