gene expression divergence is coupled to evolution of dna structure in coding regions基因表达差异耦合演化的dna结构编码区域.pdfVIP

Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions Zhiming Dai*, Xianhua Dai* School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China 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. Citation: Dai Z, Dai X (2011) Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions. PLoS Comput Biol 7(11): e1002275. doi:10.1371/journal.pcbi.1002275 Editor: Eran Segal, Weizmann Institute of Science, Israel Received February 18, 2011; Accepted October 1, 2011; Published November 17, 2011 Copyright: 2011 Dai, Dai. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are cred