PUBLICATION

Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

Authors
Woolfe, A., and Elgar, G.
ID
ZDB-PUB-070924-1
Date
2007
Source
Genome biology   8(4): R53 (Journal)
Registered Authors
Elgar, Greg, Woolfe, Adam
Keywords
none
MeSH Terms
  • Animals
  • Base Sequence
  • Conserved Sequence
  • Evolution, Molecular
  • Fish Proteins/classification
  • Fish Proteins/genetics
  • Fish Proteins/physiology
  • Gene Duplication
  • Genomics*
  • Molecular Sequence Data
  • Phylogeny
  • Regulatory Elements, Transcriptional*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Takifugu/genetics*
PubMed
17428329 Full text @ Genome Biol.
Abstract
BACKGROUND: A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis-regulatory subfunctions between paralogs following duplication (a process known as regulatory subfunctionalization). Despite a number of gene expression studies that support this mechanism, no comprehensive analysis of regulatory subfunctionalization has been undertaken at the level of the distal cis-regulatory modules involved. We have exploited fish-mammal genomic alignments to identify and compare more than 800 conserved non-coding elements (CNEs) that associate with genes that have undergone fish-specific duplication and retention. RESULTS: Using the abundance of duplicated genes within the Fugu genome, we selected seven pairs of teleost-specific paralogs involved in early vertebrate development, each containing clusters of CNEs in their vicinity. CNEs present around each Fugu duplicated gene were identified using multiple alignments of orthologous regions between single-copy mammalian orthologs (representing the ancestral locus) and each fish duplicated region in turn. Comparative analysis reveals a pattern of element retention and loss between paralogs indicative of subfunctionalization, the extent of which differs between duplicate pairs. In addition to complete loss of specific regulatory elements, a number of CNEs have been retained in both regions but may be responsible for more subtle levels of subfunctionalization through sequence divergence. CONCLUSION: Comparative analysis of conserved elements between duplicated genes provides a powerful approach for studying regulatory subfunctionalization at the level of the regulatory elements involved.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping