Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29 Jiangjun Avenue, Nanjing, Jiangsu, 211106, China.
Department of Gynecology and Obstetrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210029, China.
BMC Genomics. 2017 Oct 3;18(Suppl 6):680. doi: 10.1186/s12864-017-4029-3.
Circular RNA (circRNA) is one type of noncoding RNA that forms a covalently closed continuous loop. Similar to long noncoding RNA (lncRNA), circRNA can act as microRNA (miRNA) 'sponges' to regulate gene expression, and its abnormal expression is related to diseases such as atherosclerosis, nervous system disorders and cancer. So far, there have been no systematic studies on circRNA abundance and expression profiles in human adult and fetal tissues.
We explored circRNA expression profiles using RNA-seq data for six adult and fetal normal tissues (colon, heart, kidney, liver, lung, and stomach) and four gland normal tissues (adrenal gland, mammary gland, pancreas, and thyroid gland). A total of 8120, 25,933 and 14,433 circRNAs were detected by at least two supporting junction reads in adult, fetal and gland tissues, respectively. Among them, 3092, 14,241 and 6879 circRNAs were novel when compared to the published results. In each adult tissue type, we found at least 1000 circRNAs, among which 36.97-50.04% were tissue-specific. We reported 33 circRNAs that were ubiquitously expressed in all the adult tissues we examined. To further explore the potential "housekeeping" function of these circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network containing 17 circRNAs, 22 miRNAs and 90 mRNAs. Furthermore, we found that both the abundance and the relative expression level of circRNAs were higher in fetal tissue than adult tissue. The number of circRNAs in gland tissues, especially in mammary gland (9665 circRNA candidates), was higher than that of other adult tissues (1160-3777).
We systematically investigated circRNA expression in a variety of human adult and fetal tissues. Our observation of different expression level of circRNAs in adult and fetal tissues suggested that circRNAs might play their role in a tissue-specific and development-specific fashion. Analysis of circRNA-miRNA-mRNA network provided potential targets of circRNAs. High expression level of circRNAs in mammary gland might be attributed to the rich innervation.
环状 RNA (circRNA) 是一种形成共价闭合连续环的非编码 RNA。与长非编码 RNA (lncRNA) 相似，circRNA 可以作为 microRNA (miRNA) 的“海绵”来调节基因表达，其异常表达与动脉粥样硬化、神经系统疾病和癌症等疾病有关。到目前为止，还没有关于人类成人和胎儿组织中 circRNA 丰度和表达谱的系统研究。
我们使用六个成人和胎儿正常组织（结肠、心脏、肾脏、肝脏、肺和胃）和四个腺体正常组织（肾上腺、乳腺、胰腺和甲状腺）的 RNA-seq 数据探索 circRNA 表达谱。在成人、胎儿和腺体组织中，至少有两个支持连接读取检测到 8120、25933 和 14433 个 circRNA。其中，与已发表的结果相比，有 3092、14241 和 6879 个 circRNA 是新的。在每种成人组织类型中，我们发现至少有 1000 个 circRNA，其中 36.97-50.04%是组织特异性的。我们报道了 33 个在我们检查的所有成人组织中普遍表达的 circRNA。为了进一步探索这些 circRNA 的潜在“管家”功能，我们构建了一个包含 17 个 circRNA、22 个 miRNA 和 90 个 mRNA 的 circRNA-miRNA-mRNA 调控网络。此外，我们发现 circRNA 的丰度和相对表达水平在胎儿组织中均高于成人组织。腺体组织中的 circRNA 数量较高，尤其是乳腺（9665 个 circRNA 候选物）高于其他成人组织（1160-3777 个）。
我们系统地研究了多种人类成人和胎儿组织中的 circRNA 表达。我们观察到成人和胎儿组织中 circRNA 表达水平的不同，表明 circRNA 可能以组织特异性和发育特异性的方式发挥作用。circRNA-miRNA-mRNA 网络分析提供了 circRNA 的潜在靶点。乳腺中 circRNA 的高表达水平可能归因于丰富的神经支配。
