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

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.

Figure 1.

Comparison of the co-expression levels of three neighboring gene patterns (pairs, triplets, and quadruplets). In the upper figure, the Pearson correlation values of the three patterns and those of random pairs are used to construct their individual cumulative distributions. The lower table indicates the significance score of the KS test (p value).

Figure 2.

Comparison of the co-expression levels of four gene distance patterns (50 kbp, 100 kbp, 300 kbp and 500 kbp sliding windows). In the upper figure, the Pearson correlation values of the four patterns and those of random pairs are used to construct their individual cumulative distributions. The lower table indicates the significance score of the KS test (p value).

Figure 3.

Distribution of group sizes for various physical distances (50 kbp, 100 kbp, 300 kbp and 500 kbp sliding windows).

Figure 4.

Distribution of TLS distances (kbp) in highly co-expressed adjacent gene pairs (Pearson correlation value >0.7) and lowly co-expressed adjacent gene pairs (Pearson correlation value <0.2).

Figure 5.

Comparison of the co-expression levels of the three neighboring gene patterns without tandem repeats. The lower table indicates the significance score of the KS test (p value).