Abstract
A systematic analysis of CpG islands in ten mammalian genomes suggests that an increase in chromosome number elevates GC content and prevents loss of CpG islands.
Highlights
CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes
CpG island (CGI) and CGI density in ten mammalian genomes We first present our analysis of CGIs identified by Takai and Jones' algorithm [14] in ten mammalian genome sequences
According to gene annotations in the National Center for Biotechnology Information (NCBI) database, we identified 24,228 CGIs overlapped or within genes, 13,026 CGIs whose whole sequences were within intergenic regions, 12,136 CGIs whose whole sequences were within gene regions, and 11,192 CGIs overlapped with transcriptional start sites (TSS CGIs) in the human genome
Summary
CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Mammalian genomic DNA generally shows a great deficit of CpG dinucleotides, for example, the ratio of the observed over the expected CpGs (ObsCpG/ExpCpG) is approximately 0.20-0.25 in the human and mouse genomes [2,3,4]. This deficit is largely attributed to the hypermutability of methylated CpGs to TpGs (or CpAs in the complementary strand) [5,6]. To our best knowledge, there has been no comprehensive analysis of CGIs and their density at the DNA sequence level in mammals
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