Comprehensive Analysis Of Divergent Gene Pairs In Eukaryotic Genomes

It has long been known that the gene organization is one of the important biological information and strongly associated with gene transcriptional regulation. The most well-known example is prokaryotic operons,which ensure effective gene coregulation.Generally presumed,genes within an operon are ahnost always functional associated.Despite the rarity of an operon structure in eukaryotes,more and more evidence by comparative genomics indicate that gene order is indeed conserved during the evolution,suggesting that genes are not randomly distributed on the chromosome.The non-random gene distribution is associated with the regulation of sequence and chromosome structures and has selection advantages during the genome evolution.Divergent(or "bidirectional")gene pair is defined as two adjacent genes which are divergently transcribed on opposite strands of DNA with transcription start sites (TSSs)not more than 1000 base pairs apart.Divergent gene pairs are considered as common phenomena since lots of individual experimental evidences have been reported.Only a few genome-wide analyses have been studied in detail.The mechanism and evolution of this gene organization is of great interest because a mutation in the region between divergent gene pairs would cause changes in the promoters of both genes and affect the co-regulated transcription of the pairs.We conducted comprehensive analysis of divergent gene organization in Drosophila genomes and comparision with other eukaryotic genomes.The enrichment of divergent gene pairs was found in all the eukaryotes.However,D.melanogaster had significantly higher proportion of divergent gene pairs relative to its gene density than the other eukaryotes.The results obtained by comparative genomics indicated that the divergent gene pairs were conserved on a certain scale of evolution.The divergent gene arrangement seems to have arisen independently each other during the evolution. The expression analysis showed that most of divergent gene pairs in D.melanogaster were significantly correlated.Furthermore,divergent gene pairs were likely to have strong functional association and potential regulatory interactions.Finally,we found the divergent genes usually perform housekeeping role and have no TATA box in shared promoter region.The combination of Initiator(Inr)and Downstream Promoter Element(DPE)may play an important role in regulating the divergent gene organization in D.melanogaster,just like CpG islands for mammals.