ArticleBMC bioinformatics2003
Conservation of regulatory elements between two species of Drosophila.
Article in BMC bioinformatics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 95 citations in OpenAlex.
- Transcriptional Enhancers inGenetics · 2020Review
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.Genome biology and evolution · 2018Article
- Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.PLoS computational biology · 2014Article
- Simulations of enhancer evolution provide mechanistic insights into gene regulation.Molecular biology and evolution · 2014Article
- CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.PloS one · 2014Article
- A statistical thin-tail test of predicting regulatory regions in the Drosophila genome.Theoretical biology & medical modelling · 2013Article
- Functional characterization of motif sequences under purifying selection.Nucleic acids research · 2013Article
- Article
- Assessing computational methods of cis-regulatory module prediction.PLoS computational biology · 2010Article
- Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.Genome biology and evolution · 2010Article
- Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.BMC evolutionary biology · 2009Article
- Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.Journal of molecular evolution · 2009Article
- Different gene regulation strategies revealed by analysis of binding motifs.Trends in genetics : TIG · 2009Article
- Article
- OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.BMC bioinformatics · 2009Article
- Evolution of regulatory sequences in 12 Drosophila species.PLoS genetics · 2009Article
- Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species.PLoS biology · 2008Article
- CompMoby: comparative MobyDick for detection of cis-regulatory motifs.BMC bioinformatics · 2008Article
- Discovering gapped binding sites of yeast transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundOne of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arrangement are poorly understood. However, the genomes of suitably diverged species help to predict regulatory elements based on the generally accepted assumption that conserved blocks of genomic sequence are likely to be functional. To judge the efficacy of strategies that prefilter by sequence conservation it is important to know to what extent the converse assumption holds, namely that functional elements common to both species will fall within these conserved blocks. The recently completed sequence of a second Drosophila species provides an opportunity to test this assumption for one of the experimentally best studied regulatory networks in multicellular organisms, the body patterning of the fly embryo.
resultsWe find that 50%-70% of known binding sites reside in conserved sequence blocks, but these percentages are not greatly enriched over what is expected by chance. Finally, a computational genome-wide search in both species for regulatory modules based on clusters of binding sites suggests that genes central to the regulatory network are consistently recovered.
conclusionsOur results indicate that binding sites remain clustered for these "core modules" while not necessarily residing in conserved blocks. This is an important clue as to how regulatory information is encoded in the genome and how modules evolve.
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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.