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CpG island density and its correlations with genomic features in mammalian genomes

Leng Han123, Bing Su24, Wen-Hsiung Li5 and Zhongming Zhao16*

Author Affiliations

1 Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23298, USA

2 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

3 Graduate School, Chinese Academy of Sciences, Beijing 100039, China

4 Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

5 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

6 Department of Human Genetics and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA

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Genome Biology 2008, 9:R79  doi:10.1186/gb-2008-9-5-r79

Published: 13 May 2008



CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one genome. To date, there seems to be no comparative analysis of CpG islands and their density at the DNA sequence level among mammalian genomes and of their correlations with other genome features.


In this study, we performed a systematic analysis of CpG islands in ten mammalian genomes. We found that both the number of CpG islands and their density vary greatly among genomes, though many of these genomes encode similar numbers of genes. We observed significant correlations between CpG island density and genomic features such as number of chromosomes, chromosome size, and recombination rate. We also observed a trend of higher CpG island density in telomeric regions. Furthermore, we evaluated the performance of three computational algorithms for CpG island identifications. Finally, we compared our observations in mammals to other non-mammal vertebrates.


Our study revealed that CpG islands vary greatly among mammalian genomes. Some factors such as recombination rate and chromosome size might have influenced the evolution of CpG islands in the course of mammalian evolution. Our results suggest a scenario in which an increase in chromosome number increases the rate of recombination, which in turn elevates GC content to help prevent loss of CpG islands and maintain their density. These findings should be useful for studying mammalian genomes, the role of CpG islands in gene function, and molecular evolution.