title: Gene expression divergence is coupled to evolution of DNA structure in coding regions.
abstract: Sequence changes in coding region and regulatory region of the gene itself (cis) determine most of gene expression divergence between closely related species. But gene expression divergence between yeast species is not correlated with evolution of primary nucleotide sequence. This indicates that other factors in cis direct gene expression divergence. Here, we studied the contribution of DNA three-dimensional structural evolution as cis to gene expression divergence. We found that the evolution of DNA structure in coding regions and gene expression divergence are correlated in yeast. Similar result was also observed between Drosophila species. DNA structure is associated with the binding of chromatin remodelers and histone modifiers to DNA sequences in coding regions, which influence RNA polymerase II occupancy that controls gene expression level. We also found that genes with similar DNA structures are involved in the same biological process and function. These results reveal the previously unappreciated roles of DNA structure as cis-effects in gene expression.
authors: School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China. zhimdai@gmail.com
authors: Zhiming
authors: Z
authors: Dai
authors: Xianhua
authors: X
authors: Dai
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004330:Drosophila / Q000235:genetics; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D012045:Regulatory Sequences, Nucleic Acid; D012440:Saccharomyces / Q000235:genetics; D017422:Sequence Analysis, DNA; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors; D004247:DNA