تجزیه و تحلیل بیوانفورماتیکی غنی‌سازی مجموعه‌های ژنی در حد فاصل مراحل تسهیم و بلاستوسیست ‏توسعه جنینی گاو با استفاده از داده‌های ریز آرایه ‏DNA

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری، گروه علوم دامی، دانشگاه آزاد اسلامی واحد علوم و تحقیقات، تهران، ایران

2 استادیار، گروه علوم دامی، دانشگاه آزاد اسلامی واحد علوم و تحقیقات، تهران، ایران

3 دانشیار، گروه علوم دامی، دانشکده کشاروزی، دانشگاه یاسوج، یاسوج، ایران

4 استاد، گروه علوم دامی، دانشگاه آزاد اسلامی واحد علوم و تحقیقات، تهران، ایران

5 استادیار، گروه علوم دامی، دانشگاه آزاد اسلامی واحد شهرقدس، شهرقدس، ایران

چکیده

به منظور درک علل مرگ‌ومیر و همچنین قابلیت زنده مانی جنین گاو، شناخت مسیرهای متابولیکی و الگوهای بیان مجموعه ژنی مرتبط با مراحل حد فاصل تسهیم و بلاستوسیت ضروری  به نظر می رسد. با این انگیزه در این پژوهش مجموعه­های ژنی غنی‌سازی شده از یک سلول تخم تا مرحله 16 سلولی و بلاستوسیست در توسعه جنینی گاو مورد بررسی قرار گرفت. بدین منظور، داده‌های خام ریزآرایه DNA از پایگاه داده GEO با دسترسی آزاد، پیاده سازی شدند. سپس، کاوشگرهای متفاوت بیان، با استفاده از نرم‌افزار برخط agriGO v2.0 و به روش تحلیل غنی‌سازی تکین (SEA)، غنی‌سازی شدند. نتایج این تحقیق به‌طور خلاصه، نشان داد که در مجموع، تعداد 5 ژن؛ KPNA7، RGS2، TESC، MLLT11، BMP15 با افزایش بیان و همچنین، تعداد 5 ژن؛ KRT8، CLDN6، PLAC8، FN1، KRT18 با الگوی کاهش بیان، بیشترین میزان تفاوت بیان را نشان دادند (05/0P£). همچنین، در تجزیه و تحلیل SEA، 39 مجموعه ژنی در مسیر فرآیندهای زیستی از جمله متابولیسم­­ NADP، tRNA، ATP، و کاتابولیسم­ فسفولیپیدها، آپوپتوز و رشد سلول، گلیکولیز، میتوز، تعداد 13 مجموعه ژنی در مسیر عملکردهای مولکولی مختلف شامل یون منگنز، rRNA، فعالیت­های اکسیداسیون سیتوکرومC، فاکتور آغازین ترجمه، ATP و فعالیت ATPase و در سطح مولفه­های سلولی 12 مجموعه ژنی از جمله غشای وزیکول­های سیتوپلاسم، غشای شبکه اندوپلاسمیک، میکروتوبول و اسپیندل­ها و غشای پلاسمائی بیشترین غنی‌سازی (05/0P£) را نشان دادند. به‌عنوان نتیجه‌گیری کلی، مجموعه­های ژنی غنی‌سازی شده در بلاستوسیست نشان‌دهنده، آغاز فرآیند تمایز بین سلول‌ها و انتقال از حالت بلاستوسیست به سمت فرایند لانه­گزینی است. در نهایت، چنین به نظر می‌رسد که تفاوت الگوی بیان مجموعه­های ژنی و برهمکنش آن­ها در این مرحله احتمالاً به زنده‌ماندن یا تحلیل جنین ختم می­شود.

کلیدواژه‌ها

عنوان مقاله [English]

Bioinformatics analysis of gene sets enrichment between bovine embryonic cleavage ‎and development blastocysts using DNA microarray data

نویسندگان [English]

  • Peyman Khaje Ghiassi 1
  • Mahdi Amin Afshar 2
  • Mostafa Ghaderi Zefrehei 3
  • Naser Emam jome kashan 4
  • Mahmood Honarvar 5
1 Ph.D. Candidate, Department of Animal Sciences, Islamic Azad University, Science and Research Branch, Tehran, Iran
2 Assistant Professor, Department of Animal Sciences, Islamic Azad University, Science and Research Branch, Tehran, Iran
3 Associate Professor, Department of Animal Sciences, Faculty of Agriculture, Yasouj University, Yasouj, Iran
4 Professor, Department of Animal Sciences, Islamic Azad University, Science and Research Branch, Tehran, Iran
5 Assistant Professor, Department of Animal Sciences, Islamic Azad University, Qods City Branch, Tehran, Iran
چکیده [English]

In order to understand the causes of bovine embryo mortality and viability, it is necessary to identify different pathways between the embryonic fission and the blastocyst. The enriched sets of genes from a bovine embryonic cell to a 16-cell and blastocyst stage were examined. The raw DNA microarray data was downloaded from the GEO database. Then differentially expressed probes were enriched with the online software agriGO v2 by means of singular enrichment analysis (SEA). The results of this study showed that a total of 5 genes with increased expression, including KPNA7, RGS2, TESC, MLLT11, BMP15 and 5 genes with decreased expression, including KRT8, CLDN6, PLAC8, FN1, KRT18 had the highest differentially expressed pattern (P ≤0.05). In addition, 39 gene sets in various molecular metabolic pathways, including NADP metabolism, tRNA, ATP, phospholipid catabolism, apoptosis and cell growth, glycolysis, mitosis; 13 gene sets on the path of molecular functions, including manganese ion, RRNA, cytochrome C oxidation activities, translation primers, ATP and ATPase activity and at the level of the cellular components of 12 gene sets on the path of the cytoplasmic cavesicle membrane, endoplasmic reticulum membrane, microtubules and Spindles and plasma membrane showed the highest enrichment (P ≤0.05). As a result, the gene sets enriched with blastocysts indicate the beginning of cell differentiation and the transition from the blastocyst state to the implantation process. Ultimately, at this stage, gene sets are expressed, the interaction of which is likely to result in the survival or analysis of the embryo.

کلیدواژه‌ها [English]

  • Blastocyst
  • Cleavage
  • Gene Sets Enrichment
  • Cattle
  • Fertilization‎

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علوم دامی ایران
دوره 53، شماره 1
اردیبهشت 1401
صفحه 53-68

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  • تاریخ دریافت: 07 آذر 1400
  • تاریخ بازنگری: 15 دی 1400
  • تاریخ پذیرش: 18 دی 1400

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