采用 RNA-seq 技术鉴定沙尔和桑萨尔绵羊卵巢组织中差异表达的长非编码 RNA。

Identification of differentially expressed long noncoding RNAs in the ovarian tissue of Shal and Sangsari ewes using RNA-seq.

机构信息

Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

出版信息

Vet Med Sci. 2022 Sep;8(5):2138-2146. doi: 10.1002/vms3.859. Epub 2022 Jun 6.

DOI:10.1002/vms3.859

PMID:35667079

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9514483/

Abstract

BACKGROUND

The ovary has an important role in reproductive function. Animal reproduction is dominated by numerous coding genes and noncoding elements. Although long noncoding RNAs (LncRNAs) are important in biological activity, little is known about their role in the ovary and fertility.

METHODS

Three adult Shal ewes and three adult Sangsari ewes were used in this investigation. LncRNAs in ovarian tissue from two breeds were identified using bioinformatics analyses, and then target genes of LncRNAs were discovered. Target genes were annotated using the DAVID database, and their interactions were examined using the STRING database and Cytoscape software. The expression levels of seven LncRNAs with their target genes were assessed by real-time PCR to confirm the RNA-seq.

RESULTS

Among all the identified LncRNAs, 124 LncRNAs were detected with different expression levels between the two breeds (FDR < 0.05). According to the DAVID database, target genes were discovered to be engaged in one biological process, one cellular component, and 21 KEGG pathways (FDR < 0.05). The PES1, RPS9, EF-1, Plectin, SURF6, CYC1, PRKACA MAPK1, ITGB2 and BRD2 genes were some of the most crucial target genes (hub genes) in the ovary.

CONCLUSION

These results could pave the way for future efforts to address sheep prolificacy barriers.

摘要

背景

卵巢在生殖功能中起着重要作用。动物繁殖受众多编码基因和非编码元件控制。尽管长非编码 RNA（LncRNA）在生物活性中很重要，但它们在卵巢和生育能力中的作用知之甚少。

方法

本研究使用了三只成年沙尔羊和三只成年桑萨里羊。使用生物信息学分析鉴定了来自两个品种的卵巢组织中的 LncRNA，然后发现了 LncRNA 的靶基因。使用 DAVID 数据库对靶基因进行注释，并使用 STRING 数据库和 Cytoscape 软件检查它们的相互作用。通过实时 PCR 评估具有靶基因的七种 LncRNA 的表达水平，以确认 RNA-seq。

结果

在所鉴定的所有 LncRNA 中，在两个品种之间检测到 124 种 LncRNA 具有不同的表达水平（FDR < 0.05）。根据 DAVID 数据库，发现靶基因参与了一个生物学过程、一个细胞成分和 21 个 KEGG 途径（FDR < 0.05）。PES1、RPS9、EF-1、Plectin、SURF6、CYC1、PRKACA MAPK1、ITGB2 和 BRD2 等基因是卵巢中一些最关键的靶基因（枢纽基因）。