Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm

Abstract

Cattle supply an important source of nutrition for humans in the world. CpG islands (CGIs) are very important and useful, as they carry functionally relevant epigenetic loci for whole genome studies. As a matter of fact, there have been no formal analyses of CGIs at the DNA sequence level in cattle genomes and therefore this study was carried out to fill the gap. We used hidden markov model algorithm to detect CGIs. The total number of predicted CGIs for cattle was 90668. The number of detected CGIs and CGI densities downwardly varied across chromosomes. Chromosome 25 had the largest number of CGIs (4556) and the highest CGI density (106.20 CGIs/Mb).A significant positive correlation observed among CGI densities with guanine-cytosine (GC) content, Obs_CpG/Exp_CpG, recombination rate and gene density. When the size of chromosomes increased, the CGI densities decreased and a trend of higher CGI densities in the telomeric regions observed. This feature may be the reason of a positive correlation between CGI density and recombination rate. To detect information on CGI density differences between cattle and other vertebrate genomes, CGI density was also scanned in eleven vertebrate genomes. The CGI densities varied greatly among genomes. These discoveries may contribute to a better understanding of epigenomic role of CGIs and their molecular evolution in the cattle.