Co-expression of neighboring genes in the zebrafish (Danio rerio) genome

Int J Mol Sci. 2009 Aug 21;10(8):3658-70. doi: 10.3390/ijms10083658.

Abstract

Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson's correlation coefficient R>0.7) is low (0.24% approximately 0.67%); however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes' co-expression are also discussed.

Keywords: co-expression; gene expression; neighboring genes; promoter; zebrafish.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Genetic
  • Gene Expression Regulation*
  • Genome*
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • Transcription, Genetic
  • Zebrafish / genetics*
  • Zebrafish Proteins / genetics
  • Zebrafish Proteins / metabolism

Substances

  • Zebrafish Proteins