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% ~ 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.
Highlights
The distribution of genes in eukaryotic genomes was long believed to be random; recent studies have indicated that this is not always the case [1,2,3]
Of the 6,444 genes with expression values and their relative positions in the zebrafish genome, we found that only a small fraction of the gene pairs exhibited significant co-expression levels
The modification of the chromatin structure can be used to explain the co-expression of neighboring genes in zebrafish, as separated loci within an acetylated chromatin can be commonly regulated
Summary
The distribution of genes in eukaryotic genomes was long believed to be random; recent studies have indicated that this is not always the case [1,2,3]. Similar phenomena have been observed in Drosophila, nematodes, and yeast [10,11,12,13,14]. Among these observations, the co-expression of adjacent pairs is crucial because changes in the genome’s organization could alter the co-regulated transcription of the pairs [9,12]. Cohen et al [19] found that yeast genes of neighboring gene triplets display similar expression patterns, while Spellman and Rubin [13] reported that more than 20% of the genes in the Drosophila genome are clustered into co-regulated groups of 10-30 genes. Many neighboring gene pairs within a distance range of 20 kbp show correlated expressions [17]; and co-expression of neighboring genes has even been observed in plants, such as Arabidopsis [20,21]
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