Comparative Analysis of CpG Islands in Four Fish Genomes

Comparative and Functional Genomics - Tập 2008 - Trang 1-6 - 2008
Leng Han1,2,3, Zhongming Zhao4,5,3
1Graduate School, Chinese Academy of Sciences, Beijing 100039, China
2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
3Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
4Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
5Department of Human Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA

Tóm tắt

There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We first evaluated the performance of three popular CGI identification algorithms in four fish genomes (tetraodon, stickleback, medaka, and zebrafish). Our results suggest that Takai and Jones' (2002) algorithm is most suitable for comparative analysis of CGIs in the fish genome. Then, we performed a systematic analysis of CGIs in the four fish genomes using Takai and Jones' algorithm, compared to other vertebrate genomes. We found that both the number of CGIs and the CGI density vary greatly among these genomes. Remarkably, each fish genome presents a distinct distribution of CGI density with some genomic factors (e.g., chromosome size and chromosome GC content). These findings are helpful for understanding evolution of fish genomes and the features of fish CGIs.

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Comparative and Functional Genomics

Tập 2008

1-6

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