|
|
Research Progress of CircularRNAs |
XU Yan1, ZHAO Xue1, DU Jing-jing1, YANG Qiong2, YANG Da-hong3, PU Hong-zhou4, ZHANG Shun-hua1, ZHU Li1 |
Sichuan Agricultural University, Chengdu 611130, China |
|
|
Abstract Circular RNA (circRNA) is a novel type of endogenous noncoding RNA. Unlike linear RNAs that are terminated with 5'caps and 3'tails, circRNAs form covalently closed loop structures with neither 5'~3'polarities nor polyadenylated tails, by reverse splicing. circRNAs were typically considered to be by-products of aberrant RNA splicing due to their low levels of expression. However, with the development of RNA deep sequencing technology and bioinformatics, more circRNAs have been identified. circRNA is endogenous, abundant, conserved and stable in mammalian cells, and often show specific expression or developmental model in tissue, and there are differences in subcellular localization. Many studies have shown that circRNAs play an important role in the regulation of animal growth and development, which is also closely associated with the occurrence and development of diseases. Here, the discovery, formation, characteristics, mechanism, research methods and current research progress of circRNA were reviewed, it may contribute to further studies.
|
Received: 06 June 2017
Published: 25 October 2017
|
|
|
|
[1] |
Diener T O. Potato spindle tuber "virus":IV. A replicating, low molecular weight RNA. Virology, 1971,45(2):411-428.
|
|
|
[2] |
Hsu M, Cocaprados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature, 1979,280(5720):339-340.
|
|
|
[3] |
Qiu P C, Gaudette M F, Robinson D H, et al. Expression of the mouse testis-determining gene Sry in male preimplantation embryos. Molecular Reproduction & Development, 1995,40(2):196-204.
|
|
|
[4] |
Salzman J, Gawad C, Wang P L, et al. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. Plos One, 2012,7(2):1-12.
|
|
|
[5] |
Guo J U, Agarwal V, Guo H, et al. Expanded identification and characterization of mammalian circular RNAs. Genome Biology, 2014, 15(7):409-423.
|
|
|
[6] |
Cocquerelle C, Mascrez B, Hétuin D, et al. Mis-splicing yields circular RNA molecules. Faseb Journal Official Publication of the Federation of American Societies for Experimental Biology, 1993,7(1):155-160.
|
|
|
[7] |
Jeck W R, Sorrentino J A, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA, 2012,19(2):141-57.
|
|
|
[8] |
Kelly S, Greenman C, Cook P R, et al. Exon skipping is correlated with exon circularization. Journal of Molecular Biology, 2015,427(15):2414-2417.
|
|
|
[9] |
Zhang X O, Wang H B, Zhang Y, et al. Complementary sequence-mediated exon circularization. Cell, 2014,159(1):134-147.
|
|
|
[10] |
Ivanov A, Memczak S, Wyler E, et al. Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals. Cell Reports, 2015,10(2):170-177.
|
|
|
[11] |
Suzuki H, Zuo Y, Wang J, et al. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Research, 2006, 34(8):63-70.
|
|
|
[12] |
Zhang Y, Zhang X O, Chen T, et al. Circular Intronic Long Noncoding RNAs. Molecular Cell, 2013,51(6):792-806.
|
|
|
[13] |
Salzman J, Chen RE, Olsen M N, et al. Cell-type specific features of circular RNA expression. Plos Genetics, 2013,9(9):1-15.
|
|
|
[14] |
Xia S, Feng J, Lei L, et al. Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes. Briefings in Bioinformatics, 2016,8:1-9.
|
|
|
[15] |
Suzuki H, Tsukahara T. A view of pre-mRNA splicing from RNase R resistant RNAs.. International Journal of Molecular Sciences, 2014, 15(6):9331-9342.
|
|
|
[16] |
Bahn J H, Zhang Q, Li F, et al. The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clinical Chemistry, 2015,61(1):221-230.
|
|
|
[17] |
Werfel S, Nothjunge S, Schwarzmayr T, et al. Characterization of circular RNAs in human, mouse and rat hearts. Journal of Molecular & Cellular Cardiology, 2016,98:103-107.
|
|
|
[18] |
Pan X, Xiong K. PredcircRNA:computational classification of circular RNA from other long non-coding RNA using hybrid features. Molecular Biosystems, 2015, 11(8):2219-2226.
|
|
|
[19] |
Li Z, Huang C, Bao C, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nature Structural & Molecular Biology, 2015,22(3):256-264.
|
|
|
[20] |
Zheng Q, Bao C, Guo W, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nature Communications, 2016,7(11215):1-13.
|
|
|
[21] |
Shi X, Sun M, Liu H, et al. Long non-coding RNAs:a new frontier in the study of human diseases. Cancer Letters, 2013,339(2):159-166.
|
|
|
[22] |
Hansen T B, Jensen T I, Clausen B H, et al. Natural RNA circles function as efficient microRNA sponges. Nature, 2013,495(7441):384-388.
|
|
|
[23] |
Li F, Zhang L, Li W, et al. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/β-catenin pathway. Oncotarget, 2015,6(8):6001-6013.
|
|
|
[24] |
Ashwal-Fluss R, Meyer M, Pamudurti N R, et al. circRNA biogenesis competes with pre-mRNA splicing. Molecular Cell, 2014,56(1):55-66.
|
|
|
[25] |
Zhang Y, Zhang X O, Chen T, et al. Circular intronic long noncoding RNAs. Molecular Cell, 2013,51(6):792-806.
|
|
|
[26] |
Jeck W R, Sharpless N E. Detecting and characterizing circular RNAs. Nature Biotechnology, 2014,32(5):453-461.
|
|
|
[27] |
Fabian M R, Sonenberg N. The mechanics of miRNA-mediated gene silencing:a look under the hood of miRISC. Nature Structural & Molecular Biology, 2012,19(6):586-593.
|
|
|
[28] |
Shi X, Sun M, Liu H, et al. Long non-coding RNAs:A new frontier in the study of human diseases. Cancer Letters, 2013,339(2):159-166.
|
|
|
[29] |
Salmena L, Poliseno L, Tay Y, et al. ceRNA hypothesis:The Rosetta Stone of a hidden RNA language? Cell, 2011,146(3):353-358.
|
|
|
[30] |
Jens M. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 2013,495(7441):333-338.
|
|
|
[31] |
Chen J, Li Y, Zheng Q, et al. Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer. Cancer Letters, 2017,388:208-219.
|
|
|
[32] |
Wang K, Long B, Liu F, et al. A circular RNA protects the heart from pathological hypertrophy and heart failure by targeting miR-223. European Heart Journal, 2016,37(33):2602-2611.
|
|
|
[33] |
Qu S, Yang X, Li X, et al. Circular RNA:A new star of noncoding RNAs. Cancer Letters, 2015,365(2):141-148.
|
|
|
[34] |
Xu H, Guo S, Li W, et al. The circular RNA Cdr1as, via miR-7 and its targets, regulates insulin transcription and secretion in islet cells. Scientific Reports, 2015,5(1):12453-12465.
|
|
|
[35] |
Xue J, Liu Y, Luo F, et al. Circ100284, via miR-217 regulation of EZH2, is involved in the arsenite-accelerated cell cycle of human keratinocytes in carcinogenesis. Biochimica et Biophysica Acta, 2017,1863(3):753-763.
|
|
|
[36] |
Peng L, Chen G, Zhu Z, et al. Circular RNA ZNF609 functions as a competitive endogenous RNA to regulate AKT3 expression by sponging miR-150-5p in Hirschsprung's disease. Oncotarget, 2017,8(1):808-818.
|
|
|
[37] |
Kelemen O, Convertini P, Zhang Z, et al. Function of alternative splicing. Gene, 2013,514(1):1-30.
|
|
|
[38] |
Chen L L. The biogenesis and emerging roles of circular RNAs. Nature Reviews Molecular Cell Biology, 2016,17(4):205-211.
|
|
|
[39] |
Chao C W, Chan D C, Kuo A, et al. The mouse formin (Fmn) gene:abundant circular RNA transcripts and gene-targeted deletion analysis. Molecular Medicine, 1998,4(9):614-628.
|
|
|
[40] |
Abe N, Hiroshima M, Maruyama H, et al. Rolling circle amplification in a prokaryotic translation system using small circular RNA. Angewandte Chemie International Edition, 2013,52(27):7004-7008.
|
|
|
[41] |
Wutz A. Gene silencing in X-chromosome inactivation:advances in understanding facultative heterochromatin formation. Nature Reviews Genetics, 2011,12(8):542-553.
|
|
|
[42] |
Názer E, Lei E P. Modulation of chromatin modifying complexes by noncoding RNAs in trans. Current Opinion in Genetics & Development, 2014,25(1):68-73.
|
|
|
[43] |
Zhang Y, Yang L, Chen L L. Life without a tail:New formats of long noncoding RNAs. International Journal of Biochemistry & Cell Biology, 2013,54(1):338-349.
|
|
|
[44] |
Chuan H, Ge S. What happens at or after transcription:Insights into circRNA biogenesis and function. Transcription, 2015, 6(4):61-64.
|
|
|
[45] |
Chen L L, Yang L. Regulation of circRNA biogenesis. RNA Biology, 2015, 12(4):381-388.
|
|
|
[46] |
Perry R P, Kelley D E. Inhibition of RNA synthesis by actinomycin D:characteristic dose-response of different RNA species. Journal of Cellular Physiology, 1970, 76(2):127-139.
|
|
|
[47] |
Baroni T E, Chittur S V, George A D, et al. Advances in RIP-chip analysis:RNA-binding protein immunoprecipitation-microarray profiling. Methods in Molecular Biology, 2008, 419(419):93-108.
|
|
|
[48] |
Lukiw W. Circular RNA (circRNA) in Alzheimer's disease (AD). Frontiers in Genetics, 2013,4(4):307-308.
|
|
|
[49] |
Bachmayrheyda A, Reiner A T, Auer K, et al. Correlation of circular RNA abundance with proliferation-exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Scientific Reports, 2015,5(8057):8057-8058.
|
|
|
[50] |
Molkentin J D, Lu J R, Antos C L, et al. A calcineurin-dependent transcriptional pathway for cardiac hypertrophy. Cell, 1998,93(2):215-228.
|
|
|
[51] |
Everett A D, Tufro-Mcreddie A, Fisher A, et al. Angiotensin receptor regulates cardiac hypertrophy and transforming growth factor-beta 1 expression. Hypertension, 1994,23(5):587-592.
|
|
|
[52] |
Molkentin J D, Nd D G. Cytoplasmic signaling pathways that regulate cardiac hypertrophy. Annual Review of Physiology, 2003,63(1):391-426.
|
|
|
[53] |
Zheng C, Niu H, Li M, et al. Cyclic RNA has-circ-000595 regulates apoptosis of aortic smooth muscle cells. Molecular Medicine Reports, 2015,12(5):6656-6662.
|
|
|
[54] |
Burd C E, Jeck W R, Liu Y, et al. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet, 2010,6(12):1-15.
|
|
|
[55] |
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 Diabetologica, 2017,54(3):237-245.
|
|
|
[56] |
Qu S, Song W, Yang X, et al. Microarray expression profile of circular RNAs in human pancreatic ductal adenocarcinoma. Genomics Data, 2015, 5:385-387.
|
|
|
[57] |
Yang W, Du W W, Li X, et al. Foxo3 activity promoted by non-coding effects of circular RNA and Foxo3 pseudogene in the inhibition of tumor growth and angiogenesis. Oncogene, 2015, 35(30):3919-3931.
|
|
|
[58] |
Li P, Chen S, Chen H, et al. Using circular RNA as a novel type of biomarker in the screening of gastric cancer. Clinica Chimica Acta, 2015, 444:132-136.
|
|
|
[59] |
Tseng Y Y, Moriarity B S, Gong W, et al. PVT1 dependence in cancer with MYC copy-number increase. Nature, 2014,512(7512):82-86.
|
|
|
[60] |
Wang F, Yuan J H, Wang S B, et al. Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2. Hepatology, 2014,60(4):1278-1290.
|
|
|
[61] |
Wang X, Zhang Y, Huang L, et al. Decreased expression of hsa_circ_001988 in colorectal cancer and its clinical significances. International Journal of Clinical & Experimental Pathology, 2015,8(12):16020-16025.
|
|
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|