Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages.
Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages.
复制标题
Sus scrofa 环状 RNA 跨九个器官和三个发育阶段的全基因组分析
DOI：
10.1093/dnares/dsx022
复制
发表时间：
2017-10-01
期刊：
影响因子：
--
通讯作者：
Li K
中科院分区：
文献类型：
--
作者：
Liang G;Yang Y;Niu G;Tang Z;Li K
摘要环状RNA（circRNA）在不同器官和发育阶段的时空表达模式对于分析其功能和进化至关重要。然而，在哺乳动物中，它们在很大程度上仍然不清楚。本文对贵州小型猪（S. Scrofa），一种广泛使用的生物医学模型动物。我们鉴定了5，934个circRNA，并分析了它们的分子特性，序列保守性，时空表达模式，潜在功能以及与miRNA的相互作用。S. scrofa circRNA显示出与人类和小鼠circRNA适度的序列保守性，侧接长内含子，表现出低丰度，并且以时空特异性方式动态表达。S. scrofa circRNA在睾丸中表现出最大的丰度和复杂性。值得注意的是，31%的circRNA具有高度保守的典型miRNA种子匹配，这表明一些circRNA充当miRNA海绵。我们鉴定了149个可能与肌肉生长相关的circRNA，并发现它们的宿主基因显著参与肌肉发育、收缩、染色质修饰、阳离子稳态和ATP水解偶联质子转运;此外，这组基因显著富集了参与紧密连接和钙信号通路的基因。最后，我们构造了第一个公共S。scrofa circRNA数据库，允许研究人员查询circRNA的全面注释，表达和调控网络。
Abstract The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs. S. scrofa circRNAs show modest sequence conservation with human and mouse circRNAs, are flanked by long introns, exhibit low abundance, and are expressed dynamically in a spatio-temporally specific manner. S. scrofa circRNAs show the greatest abundance and complexity in the testis. Notably, 31% of circRNAs harbour well-conserved canonical miRNA seed matches, suggesting that some circRNAs act as miRNAs sponges. We identified 149 circRNAs potentially associated with muscle growth and found that their host genes were significantly involved in muscle development, contraction, chromatin modification, cation homeostasis, and ATP hydrolysis-coupled proton transport; moreover, this set of genes was markedly enriched in genes involved in tight junctions and the calcium signalling pathway. Finally, we constructed the first public S. scrofa circRNA database, allowing researchers to query comprehensive annotation, expression, and regulatory networks of circRNAs.
登录
查看更多内容
影响因子：
7.3
作者：
Chen, Iju;Chen, Chia-Ying;Chuang, Trees-Juen
通讯作者：
Chuang, Trees-Juen
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
4.1
作者：
Dudekulay, Dawood B.;Panda, Amaresh C.;Gorospe, Myriam
通讯作者：
Gorospe, Myriam
影响因子：
4
作者：
Hitachi K;Tsuchida K
通讯作者：
Tsuchida K
小鼠植入前胚胎中线性和环状 RNA 的单细胞 RNA-seq 转录组分析。
影响因子：
12.3
作者：
Fan X;Zhang X;Wu X;Guo H;Hu Y;Tang F;Huang Y
通讯作者：
Huang Y