Relating gene expression evolution with CpG content changes

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• 作者：Huan Yang (24)
  Dawei Li (25)
  Chao Cheng (26) (27)
  
  24. Department of Gynecology ; The Ninth People鈥檚 Hospital of Chongqing ; Chongqing ; 400700 ; China
  25. Department of Microbiology and Molecular Genetics ; College of Medicine ; Burlington ; VT ; 05405 ; USA
  26. HB7400 ; Remsen 702 ; Department of Genetics ; Geisel School of Medicine at Dartmouth ; Hanover ; NH ; 03755 ; USA
  27. Institute for Quantitative Biomedical Sciences ; Norris Cotton Cancer Center ; Geisel School of Medicine at Dartmouth ; Lebanon ; NH ; 03766 ; USA
  
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,380 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Previous studies have shown that CpG dinucleotides are enriched in a subset of promoters and the CpG content of promoters is positively correlated with gene expression levels. But the relationship between divergence of CpG content and gene expression evolution has not been investigated. Here we calculate the normalized CpG (nCpG) content in DNA regions around transcription start site (TSS) and transcription terminal site (TTS) of genes in nine organisms, and relate them with expression levels measured by RNA-seq. Results The nCpG content of TSS shows a bimodal distribution in all organisms except platypus, whereas the nCpG content of TTS only has a single peak. When the nCpG contents are compared between different organisms, we observe a different evolution pattern between TSS and TTS: compared with TTS, TSS exhibits a faster divergence rate between closely related species but are more conserved between distant species. More importantly, we demonstrate the link between gene expression evolution and nCpG content changes: up-/down- regulation of genes in an organism is accompanied by the nCpG content increase/decrease in their TSS and TTS proximal regions. Conclusions Our results suggest that gene expression changes between different organisms are correlated with the alterations in normalized CpG contents of promoters. Our analyses provide evidences for the impact of nCpG content on gene expression evolution.