The primary exploration of the structure and function of circular RNA as well as application in the investigation of tuberculosis_West China Medical Journal

Authors：

WANG Minjin ¹ ,  CHEN Xuerong ²

1. Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China;
2. Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China;

Corresponding author：

CHEN Xuerong, Email: 384481688@qq.com

Keywords：

Circular RNA; Tuberculosis; Biomarker; Bioinformatics

DOI：

10.7507/1002-0179.201807077

Video：

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Circular RNA are one kind of non-coding RNA, charactered by covalently closed rings. They can influence biological functions such as cell transduction and protein synthesis. They are associated with pathogenesis of many diseases and become a novel family of biomarkers. Now we try to introduce the origin, structure, function of circular RNA and the involved research methodology. Furthermore, we primarily discuss their application in the tuberculosis research.

Citation： WANG Minjin, CHEN Xuerong. The primary exploration of the structure and function of circular RNA as well as application in the investigation of tuberculosis. West China Medical Journal, 2018, 33(8): 1023-1027. doi: 10.7507/1002-0179.201807077 Copy

1.	Jeck WR, Sorrentino JA, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA, 2013, 19(2): 141-157.
2.	Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 2013, 495(7441): 333-338.
3.	Piwecka M, Glažar P, Hernandez-Miranda LR, et al. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science, 2017, 357(6357): eaam8526.
4.	Guo JU, Agarwal V, Guo H, et al. Expanded identification and characterization of mammalian circular RNAs. Genome Biol, 2014, 15(7): 409.
5.	Arendt T, Ueberham U, Janitz M. Non-coding transcriptome in brain aging. Aging (Albany NY), 2017, 9(9): 1943-1944.
6.	Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with pre-mRNA splicing. Mol Cell, 2014, 56(1): 55-66.
7.	Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature, 2013, 495(7441): 384-388.
8.	Vidal AF, Sandoval GT, Magalhães L, et al. Circular RNAs as a new field in gene regulation and their implications in translational research. Epigenomics, 2016, 8(4): 551-562.
9.	Ivanov A, Memczak S, Wyler E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep, 2015, 10(2): 170-177.
10.	Conn SJ, Pillman KA, Toubia J, et al. The RNA binding protein quaking regulates formation of circRNAs. Cell, 2015, 160(6): 1125-1134.
11.	Liang D, Wilusz JE. Short intronic repeat sequences facilitate circular RNA production. Genes Dev, 2014, 28(20): 2233-2247.
12.	Li Z, Huang C, Bao C, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol, 2015, 22(3): 256-264.
13.	Starke S, Jost I, Rossbach O, et al. Exon circularization requires canonical splice signals. Cell Rep, 2015, 10(1): 103-111.
14.	Hansen TB, Wiklund ED, Bramsen JB, et al. miRNA-dependent gene silencing involving ago2-mediated cleavage of a circular antisense RNA. EMBO J, 2011, 30(21): 4414-4422.
15.	Ghosal S, Das S, Sen R, et al. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front Genet, 2013, 4: 283.
16.	Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA, 2014, 20(11): 1666-1670.
17.	Dudekula DB, Panda AC, Grammatikakis I, et al. CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol, 2016, 13(1): 34-42.
18.	Zhang R, Xu J, Zhao J, et al. Silencing of hsa_circ_0007534 suppresses proliferation and induces apoptosis in colorectal cancer cells. Eur Rev Med Pharmacol Sci, 2018, 22(1): 118-126.
19.	Zhang Y, Zhang XO, Chen T, et al. Circular intronic long noncoding RNAs. Mol Cell, 2013, 51(6): 792-806.
20.	Salzman J, Gawad C, Wang PL, et al. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One, 2012, 7(2): e30733.
21.	Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression. PLoS Genet, 2013, 9(9): e1003777.
22.	Zheng Q, Bao C, Guo W, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat Commun, 2016, 7: 11215.
23.	Pamudurti NR, Bartok O, Jens M, et al. Translation of CircRNA s. Mol Cell, 2017, 66(1): 9-21.
24.	Zhuang ZG, Zhang JA, Luo HL, et al. The circular RNA of peripheral blood mononuclear cells: Hsa_circ_0005836 as a new diagnostic biomarker and therapeutic target of active pulmonary tuberculosis. Mol Immunol, 2017, 90: 264-272.
25.	Qian Z, Liu H, Li M, et al. Potential diagnostic power of blood circular RNA expression in active pulmonary tuberculosis. EBioMedicine, 2018, 27: 18-26.
26.	Huang ZK, Yao FY, Xu JQ, et al. Microarray expression profile of circular RNAs in peripheral blood mononuclear cells from active tuberculosis patients. Cell Physiol Biochem, 2018, 45(3): 1230-1240.
27.	Zhang X, Zhu M, Yang R, et al. Identification and comparison of novel circular RNAs with associated co-expression and competing endogenous RNA networks in pulmonary tuberculosis. Oncotarget, 2017, 8(69): 113571-113582.
28.	Wang M, Yang Y, Xu J, et al. CircRNA s as biomarkers of cancer: a meta-analysis. BMC Cancer, 2018, 18(1): 303.
29.	Kefas B, Godlewski J, Comeau L, et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res, 2008, 68(10): 3566-3572.
30.	Zhao Y, Alexandrov PN, Jaber V, et al. Deficiency in the ubiquitin conjugating enzyme UBE2A in Alzheimer’s disease (AD) is linked to deficits in a natural circular miRNA-7 sponge (circRNA; ciRS-7). Genes (Basel), 2016, 7(12): E116.
31.	Ouyang Q, Wu J, Jiang Z, et al. Microarray expression profile of circular RNAs in peripheral blood mononuclear cells from rheumatoid arthritis patients. Cell Physiol Biochem, 2017, 42(2): 651-659.
32.	Zhao Z, Li X, Jian D, et al. Hsa_circ_0054633 in peripheral blood can be used as a diagnostic biomarker of pre-diabetes and type 2 diabetes mellitus. Acta Diabetol, 2017, 54(3): 237-245.
33.	Zhu X, Wang X, Wei S, et al. hsa_circ_0013958: a circular RNA and potential novel biomarker for lung adenocarcinoma. FEBS J, 2017, 284(14): 2170-2182.
34.	Huang XY, Huang ZL, Xu YH, et al. Comprehensive circular RNA profiling reveals the regulatory role of the circRNA -100338/miR-141-3p pathway in hepatitis B-related hepatocellular carcinoma. Sci Rep, 2017, 7(1): 5428.
35.	López de Armentia MM, Amaya C, Colombo MI. Rab GTPases and the autophagy pathway: bacterial tagets for a suitable biogenesis and trafficking of their own vacuoles. Cells, 2016, 5(1): E11.
36.	Liu Y, Cui H, Wang W, et al. Construction of circular miRNA sponges targeting miR-21 or miR-221 and demonstration of their excellent anticancer effects on malignant melanoma cells. Int J Biochem Cell Biol, 2013, 45(11): 2643-2650.

1. Jeck WR, Sorrentino JA, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA, 2013, 19(2): 141-157.
2. Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 2013, 495(7441): 333-338.
3. Piwecka M, Glažar P, Hernandez-Miranda LR, et al. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science, 2017, 357(6357): eaam8526.
4. Guo JU, Agarwal V, Guo H, et al. Expanded identification and characterization of mammalian circular RNAs. Genome Biol, 2014, 15(7): 409.
5. Arendt T, Ueberham U, Janitz M. Non-coding transcriptome in brain aging. Aging (Albany NY), 2017, 9(9): 1943-1944.
6. Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with pre-mRNA splicing. Mol Cell, 2014, 56(1): 55-66.
7. Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature, 2013, 495(7441): 384-388.
8. Vidal AF, Sandoval GT, Magalhães L, et al. Circular RNAs as a new field in gene regulation and their implications in translational research. Epigenomics, 2016, 8(4): 551-562.
9. Ivanov A, Memczak S, Wyler E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep, 2015, 10(2): 170-177.
10. Conn SJ, Pillman KA, Toubia J, et al. The RNA binding protein quaking regulates formation of circRNAs. Cell, 2015, 160(6): 1125-1134.
11. Liang D, Wilusz JE. Short intronic repeat sequences facilitate circular RNA production. Genes Dev, 2014, 28(20): 2233-2247.
12. Li Z, Huang C, Bao C, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol, 2015, 22(3): 256-264.
13. Starke S, Jost I, Rossbach O, et al. Exon circularization requires canonical splice signals. Cell Rep, 2015, 10(1): 103-111.
14. Hansen TB, Wiklund ED, Bramsen JB, et al. miRNA-dependent gene silencing involving ago2-mediated cleavage of a circular antisense RNA. EMBO J, 2011, 30(21): 4414-4422.
15. Ghosal S, Das S, Sen R, et al. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front Genet, 2013, 4: 283.
16. Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA, 2014, 20(11): 1666-1670.
17. Dudekula DB, Panda AC, Grammatikakis I, et al. CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol, 2016, 13(1): 34-42.
18. Zhang R, Xu J, Zhao J, et al. Silencing of hsa_circ_0007534 suppresses proliferation and induces apoptosis in colorectal cancer cells. Eur Rev Med Pharmacol Sci, 2018, 22(1): 118-126.
19. Zhang Y, Zhang XO, Chen T, et al. Circular intronic long noncoding RNAs. Mol Cell, 2013, 51(6): 792-806.
20. Salzman J, Gawad C, Wang PL, et al. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One, 2012, 7(2): e30733.
21. Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression. PLoS Genet, 2013, 9(9): e1003777.
22. Zheng Q, Bao C, Guo W, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat Commun, 2016, 7: 11215.
23. Pamudurti NR, Bartok O, Jens M, et al. Translation of CircRNA s. Mol Cell, 2017, 66(1): 9-21.
24. Zhuang ZG, Zhang JA, Luo HL, et al. The circular RNA of peripheral blood mononuclear cells: Hsa_circ_0005836 as a new diagnostic biomarker and therapeutic target of active pulmonary tuberculosis. Mol Immunol, 2017, 90: 264-272.
25. Qian Z, Liu H, Li M, et al. Potential diagnostic power of blood circular RNA expression in active pulmonary tuberculosis. EBioMedicine, 2018, 27: 18-26.
26. Huang ZK, Yao FY, Xu JQ, et al. Microarray expression profile of circular RNAs in peripheral blood mononuclear cells from active tuberculosis patients. Cell Physiol Biochem, 2018, 45(3): 1230-1240.
27. Zhang X, Zhu M, Yang R, et al. Identification and comparison of novel circular RNAs with associated co-expression and competing endogenous RNA networks in pulmonary tuberculosis. Oncotarget, 2017, 8(69): 113571-113582.
28. Wang M, Yang Y, Xu J, et al. CircRNA s as biomarkers of cancer: a meta-analysis. BMC Cancer, 2018, 18(1): 303.
29. Kefas B, Godlewski J, Comeau L, et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res, 2008, 68(10): 3566-3572.
30. Zhao Y, Alexandrov PN, Jaber V, et al. Deficiency in the ubiquitin conjugating enzyme UBE2A in Alzheimer’s disease (AD) is linked to deficits in a natural circular miRNA-7 sponge (circRNA; ciRS-7). Genes (Basel), 2016, 7(12): E116.
31. Ouyang Q, Wu J, Jiang Z, et al. Microarray expression profile of circular RNAs in peripheral blood mononuclear cells from rheumatoid arthritis patients. Cell Physiol Biochem, 2017, 42(2): 651-659.
32. Zhao Z, Li X, Jian D, et al. Hsa_circ_0054633 in peripheral blood can be used as a diagnostic biomarker of pre-diabetes and type 2 diabetes mellitus. Acta Diabetol, 2017, 54(3): 237-245.
33. Zhu X, Wang X, Wei S, et al. hsa_circ_0013958: a circular RNA and potential novel biomarker for lung adenocarcinoma. FEBS J, 2017, 284(14): 2170-2182.
34. Huang XY, Huang ZL, Xu YH, et al. Comprehensive circular RNA profiling reveals the regulatory role of the circRNA -100338/miR-141-3p pathway in hepatitis B-related hepatocellular carcinoma. Sci Rep, 2017, 7(1): 5428.
35. López de Armentia MM, Amaya C, Colombo MI. Rab GTPases and the autophagy pathway: bacterial tagets for a suitable biogenesis and trafficking of their own vacuoles. Cells, 2016, 5(1): E11.
36. Liu Y, Cui H, Wang W, et al. Construction of circular miRNA sponges targeting miR-21 or miR-221 and demonstration of their excellent anticancer effects on malignant melanoma cells. Int J Biochem Cell Biol, 2013, 45(11): 2643-2650.

West China Medical Journal

The primary exploration of the structure and function of circular RNA as well as application in the investigation of tuberculosis

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