Identification of internal control genes for circular RNAs
Identification of internal control genes for circular RNAs
复制标题
环状RNA内参基因的鉴定
DOI：
10.1007/s10529-019-02723-0
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发表时间：
2019-10-01
影响因子：
2.7
通讯作者：
Feng, Jifeng
中科院分区：
文献类型：
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作者：
Zhong, Shanliang;Zhou, Siying;Feng, Jifeng
目前，还没有研究建立用于环状RNA（circRNA）分析的内部对照基因。我们的目的是确定参考circRNA的实时定量PCR（RT-qPCR. ResultsRNA-seq数据分析后，我们得到了50个circRNA，在所有样品中表达。我们根据它们的稳定性对这50种circRNA进行了排名，并获得了6种最稳定的circRNA。我们进一步评估了六种circRNA和三种线性对照基因（即，GAPDH、β-肌动蛋白和18 S rRNA）。我们的结果表明hsa_circ_0000284（circHIPK 3）和hsa_circ_0000471（circN 4 BP 2L 2）是两个最稳定的基因。去除线性RNA或包括用阿霉素、NH 4Cl和紫草素处理的细胞后，两个最稳定的基因是hsa_circ_0000471和hsa_circ_0000284。hsa_circ_0000471的扩增效率为100%，hsa_circ_0000284的扩增效率为95%。结论由于circRNA的稳定性高于线性RNA，hsa_circ_0000284和hsa_circ_0000471不仅可以作为circRNA的参考基因，也可以作为其他类型RNA的参考基因。本研究的发现填补了circRNA检测中缺乏参考基因的差距。
ObjectiveAt present, no studies have established internal control genes for circular RNA (circRNA) analyses. We aimed to identify reference circRNAs for real-time quantitative PCR (RT-qPCR).ResultsAfter analyzing the RNA-seq data, we obtained 50 circRNAs that were expressed in all samples. We ranked these 50 circRNAs according to their stability and obtained the six most stable circRNAs. We further evaluated the stability of the six circRNAs and three linear control genes (i.e., GAPDH, β-actin and 18S rRNA) in 22 cell lines. Our results indicated that hsa_circ_0000284 (circHIPK3) and hsa_circ_0000471 (circN4BP2L2) were the two most stable genes. After removing linear RNAs or including the cells treated with Adriamycin, NH4Cl and shikonin, the two most stable genes were hsa_circ_0000471 and hsa_circ_0000284. The amplification efficiency was 100% for hsa_circ_0000471 and 95% for hsa_circ_0000284.ConclusionsIn conclusion, since the stability of circRNAs is higher than that of linear RNAs, hsa_circ_0000284 and hsa_circ_0000471 may be used as reference genes not only for circRNAs but also for other kinds of RNAs. The findings in the present study fill the gap of lacking reference genes in the detection of circRNAs.