The arrangement and orientation of genes in genomes is often shaped through evolution by mechanisms such as unequal crossing over followed by random genetic drift or natural selection [1
]. Recent studies indicate that the distribution of genes in genomes does not always happen at random [3
]. In the human genome, housekeeping genes show a strong tendency to cluster together [6
], and genes that participate in the same pathway also tend to lie adjacent to each other in the genome [5
]. Moreover, several studies indicate that adjacent genes in human seem to co-express regardless of their intergenic distance [9
]. Similar phenomena have been observed in Drosophila
, nematode, and yeast [12
]. Among these observations, the co-expression of adjacent pairs is crucial because changes in such genome organization could alter the co-regulated transcription over the pairs [11
How co-expressed genes are regulated is still unclear. Two major mechanisms proposed are alterations of chromatin structure and sharing of the same regulatory elements [3
]. The open conformation of the chromatin structure is required for genes to be transcribed into RNAs and thus become expressed. A general hypothesis is that clusters of genes in the same chromatin domain have a higher chance to be expressed simultaneously than genes located in different chromatin domains [5
]. Alternatively, cis
-regulatory elements could behave like fine modules that alter gene expression locally. Therefore, adjacent pairs with common upstream activation sites (UAS) or shared regulatory systems are more likely to be co-expressed [9
Several attempts have been made to investigate the mechanism for co-expression of adjacent gene pairs. In human, the abundance of divergent pairs relative to convergent and tandem pairs has been reported [11
], and the common CpG islands that were often found between divergent pairs were known to be associated with an "open" or "active" chromatin [11
]. However, co-expressed groups of adjacent genes spanning 20–200 kilobases in the Drosophila
genome did not show any correlation with known chromosomal structures [10
]. Later, the idea of co-expression among clustered genes was rejected by Thygesen and Zwinderman [13
], whose study also failed to discover any correlation between the chromatin domain and co-expressed genes in Drosophila
It is evident that in yeast adjacent gene pairs display stronger co-expression than random pairs do [20
]. Kruglyak and Tand [12
] proposed that some co-expressed pairs resulted from sharing a single regulatory system, despite the fact that many genes controlled by separate regulatory systems may also have highly co-expressed patterns. Hurst et al.
] also concluded that divergent orientation is dominant for co-regulation and for conservation of pairs, but the finding had weak statistical support. Although these studies suggested that the sharing of a common UAS plays an important role in regulating co-expressed pairs, and that divergent pairs are more likely to share the same regulatory system, the co-expression level (defined by correlation coefficient) of divergent pairs is not significantly higher than that of tandem pairs with a similar intergenic distance [20
]. The relative contribution of the two major mechanisms to the co-expression of adjacent genes is still in debate for different organisms.
Recently, Byrnes et al.
] proposed that the majority of gene loss in yeast happened after whole-genome duplication (WGD) by single-gene deletion. Their observation implied that adjacent gene pairs were not preserved after WGD. On the other hand, several studies indicated that adjacent pairs were conserved in some organisms due to the sharing of regulatory elements [4
]. To investigate the contribution of regulatory elements to the co-expression of adjacent pairs, we first examined the conservation of adjacency in five yeast species. It is of particular interest to study the conservation of adjacent pairs using yeast species which have undergone WGD, because the duplicated adjacent relationship would in theory be free of evolutionary selection. Importantly, the advancement of technology has led to the establishment of databases of transcription factors (TF) and transcription factor binding sites (TFBSs). These tools allow researchers to investigate the mechanism for co-expression of adjacent pairs by studying sharing of common regulatory systems. Herein, we present a comprehensive examination of the intergenic regions between adjacent genes to inquire whether these pairs frequently share common TFs. Our study provides clear evidence that sharing of the common TFs is not an exclusive component of the driving force in co-regulation of adjacent gene pairs in yeast.