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Comparative analysis of vertebrate Shh genes identifies novel conserved non-coding sequence
Debbie K Goode1, Philip Snell, Greg Elgar
1Comparative Genomics Group, HGMP-Resource Centre, Hinxton, Cambridge, CB10 1SB, UK. dgoode@hgmp.mrc.ac.uk
Summary
Comparative genomics using the compact Fugu genome identified novel regulatory elements in the Sonic hedgehog (Shh) gene. This approach efficiently predicts control elements, complementing functional methods.
Area of Science:
- Genomics
- Developmental Biology
- Comparative Genomics
Background:
- The puffer fish (Takifugu rubripes, or Fugu) is a valuable model organism due to its compact genome.
- Sonic hedgehog (Shh) is a crucial protein regulating embryonic cell differentiation patterns.
Purpose of the Study:
- To sequence the Fugu Shh gene and compare it with mammalian and zebrafish orthologs.
- To identify novel conserved non-coding sequences and regulatory elements within the Fugu Shh gene.
Main Methods:
- Comparative genomics analysis of the Fugu Shh gene against mammalian and zebrafish orthologs.
- Identification of conserved non-coding sequences upstream of exon one and within introns.
Main Results:
- Novel conserved non-coding sequences were identified upstream of exon one and within the introns of the Fugu Shh gene.
- Conserved sequences helped delineate previously characterized activator regions and enhancers.
- Comparative methodology predicted new putative regulatory elements.
Conclusions:
- Comparative genomics using Fugu is a powerful tool for identifying novel regulatory elements.
- This approach complements traditional functional methods like deletion mapping for enhancer identification.