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. 2017 Oct 3;18(Suppl 6):680.
doi: 10.1186/s12864-017-4029-3.

Circular RNA expression profiles and features in human tissues: a study using RNA-seq data

Tianyi Xu  1 , Jing Wu  1 , Ping Han  2 , Zhongming Zhao  3   4 , Xiaofeng Song  5
Affiliations

Circular RNA expression profiles and features in human tissues: a study using RNA-seq data

Tianyi Xu et al. BMC Genomics. .

Abstract

Background: 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.

Results: 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).

Conclusions: 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.

Keywords: Circular RNA; Expression profile; Mammary gland; Regulatory network; Tissue specificity; microRNA ‘sponge’.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Distribution of circRNAs in human adult normal tissues. a Distribution of circRNAs by the number of supporting reads in human adult normal tissues. b Distribution of the exon number of circRNAs in human adult normal tissues. c Distribution of the circRNAs among human chromosomes of six adult human normal tissues
Fig. 2
Fig. 2
Venn diagram summarizing the circRNAs (supported by at least two reads) shared among six human adult normal tissues
Fig. 3
Fig. 3
The heatmaps of the 33 shared circRNAs and their parental mRNA expression level in six human adult normal tissues
Fig. 4
Fig. 4
CircRNA-miRNA interaction network. The network consists of 33 circRNAs and 158 miRNAs. The green node represents circRNA and the blue node represents miRNA. Edge denotes the relationship between circRNA and miRNA
Fig. 5
Fig. 5
CircRNA-miRNA-mRNA interaction network. The network consists of 17 circRNAs, 22 miRNAs and 90 mRNAs. The green node represents circRNA, the purple node represents miRNA, and the blue node represents mRNA. Edge denotes their relationship
Fig. 6
Fig. 6
Distribution of circRNAs in human fetal normal tissues. a Venn diagram summarizing the circRNAs (supported by at least two reads) shared among the human fetal tissues. b Comparison of the number of circRNAs (supported by at least two reads) in adult and fetal tissues
Fig. 7
Fig. 7
Distribution of circRNAs in adult gland normal tissues. a Venn diagram summarizing the circRNAs (supported by at least two reads) shared among the four human gland tissues. b Heatmap showing the circRNA expression in each sample of adrenal gland, mammary gland, pancreas and thyroid gland
Fig. 8
Fig. 8
Heatmap showing the expression of the 56 common circRNAs and their parental mRNAs in gland normal tissues
Fig. 9
Fig. 9
Heatmap showing the expression of the 14 shared circRNA in each sample of adult tissues and gland tissues
See this image and copyright information in PMC

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