Comparative Analysis of CpG Islands in Four Fish Genomes

Leng Han,Zhongming Zhao

doi:10.1155/2008/565631

Abstract

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.

Highlights

CpG islands (CGIs) are clusters of CpG dinucleotides in GC-rich regions, usually ∼1 kb long [1]
We evaluated whether the three major algorithms could reliably identify CGIs in fish genomes
We found that the number of CGIs and the CGI density varied greatly in these fish genomes

Summary

Introduction

CGIs are clusters of CpG dinucleotides in GC-rich regions, usually ∼1 kb long [1]. They are identified in the promoter regions of approximately 50% of genes in vertebrate genomes and are considered gene markers. CpG islands are usually unmethylated in a genome, especially in the promoter regions [2], in contrast, ∼80% of CpG dinucleotides in the mammalian genomes are methylated [2, 3]. Weber et al [6] found an association of DNA methylation in CpG-poor promoters in the germline with an increased loss of CpG dinucleotides, implying that characteristics of the CGIs have been weakened or even vanished in the course of evolution. Methylation of promoter-associated CpG islands has been found to play an important role in gene silencing, genomic imprinting, Xchromosome inactivation, and carcinogenesis [7, 8]

Methods

Results

Conclusion