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Updated: Jun 1, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
Genome-wide identification of conserved regulatory function in diverged sequences
Leila Taher1, David M McGaughey, Samantha Maragh
1Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Scientists found that conserved transcription factor binding site (TFBS) arrangements can identify functional gene regulatory elements even with DNA sequence divergence. This reveals "covert" elements crucial for conserved gene regulation across species.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Gene regulatory elements can evolve significantly without losing function.
- Functional information is often maintained by conserved transcription factor binding site (TFBS) composition within regulatory regions.
Purpose of the Study:
- To develop a computational method for identifying functional noncoding orthologs with diverged DNA sequences.
- To discover evolutionarily conserved regulatory elements that lack overt sequence similarity.
Main Methods:
- Developed a method to identify functional noncoding orthologs by searching for conserved TFBS arrangements in syntenic loci.
- Applied the method to human and zebrafish genomes, analyzing approximately 3000 loci.
- Validated predictions using experimentally characterized human enhancers.
Main Results:
- Identified approximately 300 pairs of diverged elements likely sharing common ancestry and regulatory activity with a 5% false-positive rate.
- 88% of predicted functional orthologs of human enhancers retained in vivo regulatory control.
- 71% of assayed enhancer pairs showed concordant expression patterns between orthologs.
Conclusions:
- TFBS composition is critical for retaining regulatory function, even with substantial DNA sequence divergence.
- Identified a novel class of functionally conserved, evolutionarily diverged regulatory elements termed "covert" elements.
- The developed method accurately predicts regulatory function based on conserved TFBS arrangements, independent of overall sequence conservation.
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