نوع مقاله : مقاله پژوهشی
نویسندگان
1 گروه علوم دامی، دانشگاه علوم کشاورزی و منابع طبیعی خوزستان، اهواز، ایران
2 دانشیار دانشکدۀ علوم دامی و صنایع غذایی، دانشگاه کشاورزی و منابع طبیعی رامین خوزستان
3 استاد،دانشگاه علوم کشاورزی و منابع طبیعی رامین، تخصص: ژنتیک و اصلاح نژاد دام و طیور
4 دانشگاه علوم کشاورزی و منابع طبیعی خوزستان، تخصص: تغذیه نشخوارکنندگان/گاو شیری/ گوسفند/گاومیش/ روشهای آزمایشگاهی/ کشت پیوسته دو
5 دانشیار،پردیس ابوریحان، تخصص: ژنتیک و اصلاح نژاد دام/ ژنتیک مولکولی/ بیوانفورماتیک
چکیده
هدف این پژوهش شناسایی lncRNAهای دخیل در کنترل فعالیت مسیرهای بیولوژیکی مؤثر در بروز اسیدوز بود. به این منظور دو گروه گوساله شامل گروه شاهد (3 گوساله نر سالم) و گروه بیمار (3 گوساله نر مبتلا به اسیدوز) به‌صورت مقایسهای مورد مطالعه قرار گرفتند. توالی‌یابی جفتی با استفاده از پلاتفرم illumine Hiseq2500 انجام شد. از نرم‌افزار Hisat2 برای هم‌ترازی خوانشها با ژنوم مرجع گاو و بسته نرم‌افزاری StringTie جهت سرهمبندی رونوشتها استفاده شد. با استفاده از توالی‌یابی نسل بعد، 1636 ژن متعلق به lncRNAهای شناخته‌شده بین ژنی شناسایی شد که تغییرات بیان 56 ژن معنیدار بود (05/0P≤). ژنهای همجوار lncRNAهای شناخته‌شده بین ژنی روی ژنوم گاو هلشتاین تعیین شدند. نتایج نشان داد با سطح احتمال 05/0P≤، پنج مسیر بیولوژیکی Apelin signaling pathway، Gap junction، Glucagon signaling pathway، Renin secretion وAGE-RAGE signaling pathway in diabetic complications غنی میشوند. آنالیز عملکرد مولکولی این ژنها نشان داد دو عملکرد مولکولی شامل gap junction channel activity و phosphatidylinositol phospholipase C activity به‌طور معنیدار غنی میشوند. برخی lncRNAها در نمونههای سالم و اسیدوزی بیان متفاوتی داشتند و کاهش pH به‌عنوان محرکی برای فعال‌شدن برخی مسیرهای بیولوژیکی ترارسانی پیام عمل کرد. براساس نتایج حاصل، lncRNAهایی که تفاوت بیان معنیدار در گروه کنترل و اسیدوز دارند با مسیرهای مرتبط با سوخت‌وساز انرژی شکمبه و ترارسانی پیام همراه می‌باشند. از lncRNAها میتوان به‌عنوان عامل پیش‌آگاهی‌دهنده اسیدوز و بیومارکر در اصلاح دام استفاده نمود.
کلیدواژه‌ها
عنوان مقاله [English]
Biological pathways related to known intergenic lncRNAs in calf ruminal samples affected with acidosis
نویسندگان [English]
- Bizhan Mahmoudi 1
- Hedayatollah Roshanfekr 3
- Mohsen Sari 4
- Mohammad Reza Bakhtiarizadeh 5
1 Department of Animal science, Agricultural Sciences and Natural Resources University of Khuzestan, Ahvaz, Iran
2
3 Department of Animal science, Agricultural Sciences and Natural Resources University of Khuzestan, Ahvaz, Iran
4 Animal Science Department, Agricultural Sciences and Natural Resources University of Khuzestan, Ahvaz, Iran.
5 Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
چکیده [English]
The objective of this study was to identify known intergenic lncRNAs related to biological pathways of acidosis in Holstein calves using ruminal
tissue. Two groups of healthy calves (N=3) and affected by acidosis (N=3) were compared. Paired-end sequencing method was performed using the
Hiseq2500 illumine platform. Hisat2 software was used to align reads to the bovine reference genome and StringTie software package was used to
assemble read files into transcripts. Using next generation sequencing, 1636 genes belonging to known intergenic lncRNAs were identified, of which
56 genes showed significant differential expression (P≤0.05). Neighbor genes of known intergenic lncRNAs were determined on bovine genome.
Analysis of biological pathways and molecular function showed that five biological pathways were significantly (P≤0.05) enriched. These pathways
were Apelin signaling pathway, Gap junction, Glucagon signaling pathway, Renin secretion, and AGE-RAGE signaling pathway. Moreover, two
molecular functions including gap junction channel activity, and phosphatidyl inositol phospholipase C activity were significantly (P≤0.05) enriched.
Some lncRNAs have different expression in healthy and acidosis samples, and the decreased pH acts as a stimulus to activate some biological
signaling pathways. In conclusion, it was indicated that lncRNAs with differential expression between the control group and the group affected by
acidosis are associated with pathways related to rumen energy metabolism and signaling. Identified differentially expressed lncRNAs could be used as
prognostic in acidosis and biomarkers or promising candidates in animal breeding.
کلیدواژه‌ها [English]
- Gene expression pattern
- Illumine
- LncRNA
- Sequencing
- Signaling
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