MBE Advance Access originally published online on June 24, 2007
Molecular Biology and Evolution 2007 24(9):1991-2000; doi:10.1093/molbev/msm128
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Articles |
Features and Trend of Loss of Promoter-Associated CpG Islands in the Human and Mouse Genomes
,
,1
* Department of Psychiatry and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
Graduate School, Chinese Academy of Sciences, Beijing, China
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
E-mail: zzhao{at}vcu.edu.
Accepted for publication June 18, 2007.
CpG islands (CGIs) are often considered as gene markers, but the number of CGIs varies among mammalian genomes that have similar numbers of genes. In this study, we investigated the distribution of CGIs in the promoter regions of 3,197 human-mouse orthologous gene pairs and found that the mouse genome has notably fewer CGIs in the promoter regions and less pronounced CGI characteristics than does the human genome. We further inferred CGI's ancestral state using the dog genome as a reference and examined the nucleotide substitution pattern and the mutational direction in the conserved regions of human and mouse CGIs. The results reveal many losses of CGIs in both genomes but the loss rate in the mouse lineage is two to four times the rate in the human lineage. We found an intriguing feature of CGI loss, namely that the loss of a CGI usually starts from erosion at the both edges and gradually moves towards the center. We found functional bias in the genes that have lost promoter-associated CGIs in the human or mouse lineage. Finally, our analysis indicates that the association of CGIs with housekeeping genes is not as strong as previously estimated. Our study provides a detailed view of the evolution of promoter-associated CGIs in the human and mouse genomes and our findings are helpful for understanding the evolution of mammalian genomes and the role of CGIs in gene function.
Key Words: CpG island evolution • promoter • DNA methylation • functional bias • human • mouse
1 These authors contributed equally to this work
Naoko Takezaki, Associate Editor
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. G. Dineen, A. Wilm, P. Cunningham, and D. G. Higgins High DNA melting temperature predicts transcription start site location in human and mouse Nucleic Acids Res., December 1, 2009; 37(22): 7360 - 7367. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Elango and S. V. Yi DNA Methylation and Structural and Functional Bimodality of Vertebrate Promoters Mol. Biol. Evol., August 1, 2008; 25(8): 1602 - 1608. [Abstract] [Full Text] [PDF]
|
|