Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features
CpG islands (CGIs) are an important group of CpG dinucleotides in the guanine- and cytosine-rich regions as they harbour functionally relevant epigenetic loci for whole genome studies. As a matter of fact, since there has not been a formal comparative analysis of CGIs in domestic even-toed ungulate...
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| Language: | English |
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Czech Academy of Agricultural Sciences
2016-11-01
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| Series: | Czech Journal of Animal Science |
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| Online Access: | https://cjas.agriculturejournals.cz/artkey/cjs-201611-0001_genome-wide-analysis-of-cpg-islands-in-some-livestock-genomes-and-their-relationship-with-genomic-features.php |
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| author | A. Barazandeh M.R. Mohammadabadi M. Ghaderi-Zefrehei H. Nezamabadi-pour |
| author_facet | A. Barazandeh M.R. Mohammadabadi M. Ghaderi-Zefrehei H. Nezamabadi-pour |
| author_sort | A. Barazandeh |
| collection | DOAJ |
| description | CpG islands (CGIs) are an important group of CpG dinucleotides in the guanine- and cytosine-rich regions as they harbour functionally relevant epigenetic loci for whole genome studies. As a matter of fact, since there has not been a formal comparative analysis of CGIs in domestic even-toed ungulate genomes, this study was performed to serve this comparison. The Hidden Markov Model was used to detect CGIs in the genomes. The results indicated that the CGIs number and CGI densities had scant variations across genomes. The goat genome had the highest number of CGIs (99 070), whereas the alpaca genome had the highest CGI density (43.39 CGIs/Mb). Significant positive correlations were observed among CGI densities with chromosome pair number, observed CpG/expected 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 was observed. Only 10.96% of CGIs were methylated underscoring this postulation that the majority of CGIs remains to be unmethylated. The highest amount of the methylated CGIs was observed in the introns, intergenic, and coding (CDS) regions and the lowest amount of the methylated CGIs was observed in the promoter regions, implying that the DNA methylation of CGIs may control gene expression at the genome level. Detected differences between even-toed ungulate and other vertebrate genomes showed that CGI densities varied greatly among the genomes. These findings would contribute to better understanding the even-toed ungulate (epi) genomes, the role of CGIs in epigenomic functions and molecular evolution. |
| first_indexed | 2024-04-10T08:25:42Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1212-1819 1805-9309 |
| language | English |
| last_indexed | 2024-04-10T08:25:42Z |
| publishDate | 2016-11-01 |
| publisher | Czech Academy of Agricultural Sciences |
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| series | Czech Journal of Animal Science |
| spelling | doaj.art-02a5f6403167425c8a927b34cc1752552023-02-23T03:33:24ZengCzech Academy of Agricultural SciencesCzech Journal of Animal Science1212-18191805-93092016-11-01611148749510.17221/78/2015-CJAScjs-201611-0001Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic featuresA. Barazandeh0M.R. Mohammadabadi1M. Ghaderi-Zefrehei2H. Nezamabadi-pour3Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, IranDepartment of Animal Science, Shahid Bahonar University of Kerman, Kerman, IranDepartment of Animal Science, University of Yasouj, Yasouj, IranDepartment of Electrical Engineering, Shahid Bahonar University of Kerman, Kerman, IranCpG islands (CGIs) are an important group of CpG dinucleotides in the guanine- and cytosine-rich regions as they harbour functionally relevant epigenetic loci for whole genome studies. As a matter of fact, since there has not been a formal comparative analysis of CGIs in domestic even-toed ungulate genomes, this study was performed to serve this comparison. The Hidden Markov Model was used to detect CGIs in the genomes. The results indicated that the CGIs number and CGI densities had scant variations across genomes. The goat genome had the highest number of CGIs (99 070), whereas the alpaca genome had the highest CGI density (43.39 CGIs/Mb). Significant positive correlations were observed among CGI densities with chromosome pair number, observed CpG/expected 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 was observed. Only 10.96% of CGIs were methylated underscoring this postulation that the majority of CGIs remains to be unmethylated. The highest amount of the methylated CGIs was observed in the introns, intergenic, and coding (CDS) regions and the lowest amount of the methylated CGIs was observed in the promoter regions, implying that the DNA methylation of CGIs may control gene expression at the genome level. Detected differences between even-toed ungulate and other vertebrate genomes showed that CGI densities varied greatly among the genomes. These findings would contribute to better understanding the even-toed ungulate (epi) genomes, the role of CGIs in epigenomic functions and molecular evolution.https://cjas.agriculturejournals.cz/artkey/cjs-201611-0001_genome-wide-analysis-of-cpg-islands-in-some-livestock-genomes-and-their-relationship-with-genomic-features.phpeven-toed ungulate(epi) genomichidden markov modeldna methylation |
| spellingShingle | A. Barazandeh M.R. Mohammadabadi M. Ghaderi-Zefrehei H. Nezamabadi-pour Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features Czech Journal of Animal Science even-toed ungulate (epi) genomic hidden markov model dna methylation |
| title | Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features |
| title_full | Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features |
| title_fullStr | Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features |
| title_full_unstemmed | Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features |
| title_short | Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features |
| title_sort | genome wide analysis of cpg islands in some livestock genomes and their relationship with genomic features |
| topic | even-toed ungulate (epi) genomic hidden markov model dna methylation |
| url | https://cjas.agriculturejournals.cz/artkey/cjs-201611-0001_genome-wide-analysis-of-cpg-islands-in-some-livestock-genomes-and-their-relationship-with-genomic-features.php |
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