Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm
محورهای موضوعی : CamelA. برازنده 1 , م.ر. محمدآبادی 2 , م. قادری 3 , ح. نظام آبادی پور 4
1 - Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran|Department of Animal Science, University of Jiroft, Jiroft, Iran
2 - Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
3 - Department of Animal Science, University of Yasouj, Yasouj, Iran
4 - Department of Electrical Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
کلید واژه: cattle, genome, CpG islands, epigenomic, HMM,
چکیده مقاله :
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, ObsCpG/ExpCpG, 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.
گاو یکی از مهمترین تأمین کنندههای مواد غذایی و مغذی بشر در جهان است. جزایر CpG نواحی مهم و مفیدی هستند که دارای ارتباط عملکردی با رویدادهای مهم اپی ژنتیکی در سطح ژنوم میباشند. با توجه به اینکه تاکنون جزایر CpG در سطح ژنوم گاو بررسی نشدهاند هدف از این مطالعه بررسی این جزایر در ژنوم گاو با استفاده از مدلهای محفی مارکوف است. تعداد 90668 جزیره CpG در ژنوم گاو پیشبینی گردید. تغییرات تعداد و تراکم جزایر CpG در طول کروموزومها بسیار کم بود. کروموزوم 25 دارای بیشترین تعداد (4556) و تراکم (CGIs/Mb 106٫20) جزایر CpG بود. همبستگی مثبت و معنیدار بین تراکم جزایر CpG با محتوی GC، نسبت مشاهده شده به مورد انتظار CpG، نرخ نوترکیبی و تراکم ژن مشاهده گردید. با افزایش سایز کروموزمها تراکم جزایر CpG کاهش یافت و همچنین تراکم جزایر CpG در نواحی تلومری کروموزمها بیشتر از سایر قسمتها مشاهده گردید که میتواند علت همبستگی مثبت بین نرخ نوترکیبی و تراکم جزایر CpG باشد. جهت یافتن تفاوتهای جزایر CpG بین ژنوم گاو و سایر مهرهداران جزایر CpG در یازده مهرهدار دیگر بررسی گردید. تغییرات تراکم جزایر CpG در بین حیوانات مورد مطالعه بسیار متفاوت بود. یافتههای این مطالعه میتواند در درک بهتر نقش اپی ژنتیکی و نقش تکامل مولکولی جزایر CpG در ژنوم گاو مؤثر باشد.
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