Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome Public Deposited

Downloadable Content

Download PDF
  • Mezey, Jason G
    • Other Affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
  • Nuzhdin, Sergey V
    • Other Affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
  • Ye, Fangfei
    • Other Affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
  • Jones, Corbin
    • Affiliation: College of Arts and Sciences, Department of Biology, School of Medicine, Carolina Center for Genome Sciences
  • Abstract Background Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. This organization of transcriptomes suggests that coordinated evolution of gene expression for clustered genes may also be common. Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution. Results We used a common microarray platform to measure gene expression in seven closely related species in the Drosophila melanogaster subgroup, accounting for confounding effects of sequence divergence. To summarize the correlation structure among genes in a chromosomal region, we analyzed the fraction of variation along the first principal component of the correlation matrix. We analyzed the correlation for blocks of consecutive genes to assess patterns of correlation that may be manifest at different scales of coordinated expression. We find that expression of physically clustered genes does evolve in a coordinated manner in many locations throughout the genome. Our analysis shows that relatively few of these clusters are near heterochromatin regions and that these clusters tend to be over-dispersed relative to the rest of the genome. This suggests that these clusters are not the byproduct of local gene clustering. We also analyzed the pattern of co-expression among neighboring genes within a single Drosophila species: D. simulans. For the co-expression clusters identified within this species, we find an under-representation of genes displaying a signature of recurrent adaptive amino acid evolution consistent with previous findings. However, clusters displaying co-evolution of expression among species are enriched for adaptively evolving genes. This finding points to a tie between adaptive sequence evolution and evolution of the transcriptome. Conclusion Our results demonstrate that co-evolution of expression in gene clusters is relatively common among species in the D. melanogaster subgroup. We consider the possibility that local regulation of expression in gene clusters may drive the connection between adaptive sequence and coordinated gene expression evolution.
Date of publication
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Jason G Mezey et al.; licensee BioMed Central Ltd.
Journal title
  • BMC Evolutionary Biology
Journal volume
  • 8
Journal issue
  • 1
Page start
  • 2
  • English
Is the article or chapter peer-reviewed?
  • Yes
  • 1471-2148
Bibliographic citation
  • BMC Evolutionary Biology. 2008 Jan 07;8(1):2
  • Open Access
  • BioMed Central Ltd

This work has no parents.