Characterization of circular RNAs in human, mouse and rat hearts
Characterization of circular RNAs in human, mouse and rat hearts
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DOI：
10.1016/j.yjmcc.2016.07.007
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发表时间：
2016-09-01
影响因子：
5
通讯作者：
Engelhardt, Stefan
中科院分区：
文献类型：
--
作者：
Werfel, Stanislas;Nothjunge, Stephan;Engelhardt, Stefan
深度测序技术和先进的数据分析方法最近能够对来自许多组织和生物体的数千种环状 RNA 同工型 (circRNA) 进行表征。越来越多的证据表明，一些 circRNA 可能具有重要的生物学功能或在疾病条件下充当诊断生物标志物。为了分析心脏中的 circRNA 表达及其在不同条件下的变化，我们对大鼠（新生儿和成人）、小鼠（假手术或横主动脉缩窄后，TAC）和人类（失败、非失败）的核糖体耗尽文库进行了 RNA-Seq 分析。所有样本均在使用核酸外切酶 RNase R 处理或模拟处理后进行测序，每个物种均检测到超过 9000 个候选 circRNA。此外，我们还单独分离了原代心肌细胞中的核和细胞质 RNA 以及与内源性 argonaute 2 (Ago2) 相互作用的免疫共沉淀 RNA。我们发现与线性转录本相比，circRNA 在细胞质中显着富集，并且与 Ago2 具有相似的关联水平。值得注意的是，在所有三个物种中，我们观察到数十个源自 titin (Ttn) 基因的 circRNA，已知该基因在心脏成熟过程中经历高度复杂的选择性剪接。相应地，我们观察到新生和成年大鼠心脏之间 Ttn circRNA 的广泛差异调节，这表明 circRNA 的形成可能参与 titin 剪接的调节。我们期望我们的心脏 circRNA 清单以及它们的保守性和差异表达信息将为进一步研究其作为生物标志物的功能和适用性提供重要基础。 (C) 2016 年作者。由爱思唯尔有限公司出版
Deep sequencing techniques and advanced data analysis methods recently enabled the characterization of thousands of circular RNA isoforms (circRNAs) from a number of tissues and organisms. There is emerging evidence that some circRNAs may have important biological functions or serve as diagnostic biomarkers in disease conditions.In order to analyze circRNA expression in the heart and its changes in different conditions we performed RNA-Seq analysis of ribosome-depleted libraries from rats (neonatal and adult), mice (sham or after transverse aortic constriction, TAC) and humans (failing, non-failing). All samples were sequenced after treatment with exonuclease RNase R or a mock treatment and >9000 candidate circRNAs were detected for each species. Additionally, we performed separate isolation of nuclear and cytoplasmic RNA and co-immunoprecipitated RNA interacting with endogenous argonaute 2 (Ago2) in primary cardiac myocytes. We found circRNAs to be significantly enriched in the cytoplasm compared to linear transcripts and to have a similar level of association with Ago2.Notably in all three species we observed dozens of circRNAs arising from the titin (Ttn) gene, which is known to undergo highly complex alternative splicing during heart maturation. Correspondingly we observed extensive differential regulation of Ttn circRNAs between neonatal and adult rat hearts, suggesting that circRNA formation could be involved in the regulation of titin splicing.We expect that our inventory of cardiac circRNAs, as well as the information on their conservation and differential expression will provide an important basis for further studies addressing their function and suitability as biomarkers. (C) 2016 The Authors. Published by Elsevier Ltd.