Genome biology · 2007 · 27 citations · 113 references
Life SciencesBioinformaticsGeneticsComparative GenomicsGene ExpressionGenomicsCis-regulatory ElementsEnhancer ArchitectureEnhancer FunctionGene Regulatory ElementsRegulatory GenomicsCis-regulatory Element RegulationCis-regulatory EvolutionCis-regulatory ModulesConserved Regulatory ElementsEnhancer ConservationEnhancer Core ArchitectureEnhancersTissue-specific Enhancers
A systematic approach is described for analysis of evolutionarily conserved cis-regulatory DNA using cis-Decoder, a tool for discovery of conserved sequence elements that are shared between similarly regulated enhancers. Analysis of 2,086 conserved sequence blocks (CSBs), identified from 135 characterized enhancers, reveals most CSBs consist of shorter overlapping/adjacent elements that are either enhancer type-specific or common to enhancers with divergent regulatory behaviors. Our findings suggest that enhancers employ overlapping repertoires of highly conserved core elements.
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<tt>BLAT</tt>—The <tt>BLAST</tt>-Like Alignment Tool
W. James Kent · Genome Research · 2002 · 8.4K citations · Full text
Evidence for stabilizing selection in a eukaryotic enhancer element
Michael Ludwig, Casey Bergman, Nipam H. Patel et al. · Nature · 2000 · 589 citations