Proper control of gene expression is central for the unique phenotype of each organism. Phenotypic diversity can be generated through changes in gene expression. Divergence in gene expression of a specific gene between closely related species can result from sequence changes in its coding region and regulatory region (cis), or from changes in sequences or expression of its direct or indirect upstream regulators (trans). The binding of transcription factors (TFs) to sequence-specific sites in gene upstream regions plays a very important role in regulation of gene expression. Changes in TF-binding sequences and changes in abundance and binding domains of TFs can influence TF binding, which may cause variation in gene expression. The divergence of gene expression is also coupled to that of gene sequences in multicellular organisms 
. In addition, as chromatin structure is critical for the regulation of gene expression, gene expression divergence between species correlates with divergence of nucleosomal organization 
. Nucleosome positioning is determined by cis effects (i.e. the intrinsic DNA sequence preference for nucleosome), and trans effects (e.g. chromatin modifiers).
The effects of cis and trans regulation on gene expression divergence can be measured by comparison of different strains of the same species 
and by analysis of hybrid species 
. Experiments on specific genes have revealed that the contribution of cis regulation to gene expression divergence between Drosophila
species is much greater than that of trans regulation 
. A genome-wide study on yeast species has also reproduced similar observation 
. Cis-regulatory changes in gene expression are supposed to be driven by sequence mutations in TF binding sites or those in coding regions. However, most mutations in TF-binding sequences between yeast species have only little effect on gene expression divergence 
, though it cannot rule out the possibility that backup mechanisms exist among TF binding. Moreover, evolution of gene sequence in coding regions and gene expression divergence are not correlated in yeast 
. These results leave open the question of what drive gene expression divergence in cis.
The three-dimensional structure of DNA, which reflects the physicochemical and conformational properties of DNA, is critical for the packaging of DNA in the cell 
. The structure of DNA has been recognized to be important for protein-DNA recognition 
. Specific proteins-DNA interactions are fundamental to many biological processes, such as transcription, recombination, and DNA replication. DNA bending plays a role in the regulation of prokaryotic transcription 
. DNA structure can be used as discriminatory information to identify core-promoter regions 
. Specific replication-related proteins show a preference to bind curved DNA sequences 
. DNA curvature is also involved in the binding of recombination-related proteins 
A recent study has found that DNA structure in the human genome is more evolutionary constrained than the primary nucleotide sequence alone 
. Moreover, the DNA structure-conserved regions correlate with non-coding regulatory elements, better than sequence-conserved regions identified solely on the basis of primary sequence 
. These results indicate that DNA structure is important for regulation of gene expression. We presume that DNA structure is an ideal candidate for directing gene expression divergence in cis.
We evaluated DNA structure in terms of various physicochemical and conformational properties. We found that high levels of cis-driven gene expression divergence between yeast species correspond to high evolution rates of DNA structure in coding regions. This result also holds true between Drosophila species. The relationships of various types of structural evolution with gene expression divergence are conserved between yeast and Drosophila. We next investigated whether DNA structure is associated with gene characteristics. Genes that differ in DNA structure are distinguished by chromatin remodeler occupancy and histone modification levels, indicating that DNA structure influences gene expression by regulating the binding of chromatin regulators to DNA. Genes with similar DNA structures tend to belong to the same biological process and function.