Integration of Bioinformatic Predictions and Experimental Data to Identify CircRNA-miRNA Associations

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2019 Aug 28

PMID 31450634

Citations 47

Authors

Martina Dori

Silvio Bicciato

Affiliations

Soon will be listed here.

Abstract

Circular RNAs (circRNAs) have recently emerged as a novel class of transcripts, characterized by covalently linked 3'-5' ends that result in the so-called backsplice junction. During the last few years, thousands of circRNAs have been identified in different organisms. Yet, despite their role as disease biomarker started to emerge, depicting their function remains challenging. Different studies have shown that certain circRNAs act as miRNA sponges, but any attempt to generalize from the single case to the "circ-ome" has failed so far. In this review, we explore the potential to define miRNA "sponging" as a more general function of circRNAs and describe the different approaches to predict miRNA response elements (MREs) in known or novel circRNA sequences. Moreover, we discuss how experiments based on Ago2-IP and experimentally validated miRNA:target duplexes can be used to either prioritize or validate putative miRNA-circRNA associations.

Citing Articles

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Computational approaches for circRNAs prediction and in silico characterization.

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Circ-Bnc2 alleviates neuroinflammation in LPS-stimulated microglial cells to inhibit neuron cell apoptosis through regulating miR-497a-5p/HECTD1 axis.

Chen Y, Cao P Brain Behav. 2023; 13(5):e2935.

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Circular RNA regulation and function in drug seeking phenotypes.

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References

Kosik K . Molecular biology: Circles reshape the RNA world. Nature. 2013; 495(7441):322-4. DOI: 10.1038/nature11956. View

Ivanov A, Memczak S, Wyler E, Torti F, Porath H, Orejuela M . Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep. 2015; 10(2):170-7. DOI: 10.1016/j.celrep.2014.12.019. View

Dori M, Haj Abdullah Alieh L, Cavalli D, Massalini S, Lesche M, Dahl A . Sequence and expression levels of circular RNAs in progenitor cell types during mouse corticogenesis. Life Sci Alliance. 2019; 2(2). PMC: 6441494. DOI: 10.26508/lsa.201900354. View

Moore M, Scheel T, Luna J, Park C, Fak J, Nishiuchi E . miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. Nat Commun. 2015; 6:8864. PMC: 4674787. DOI: 10.1038/ncomms9864. View

Ragan C, Goodall G, Shirokikh N, Preiss T . Insights into the biogenesis and potential functions of exonic circular RNA. Sci Rep. 2019; 9(1):2048. PMC: 6376117. DOI: 10.1038/s41598-018-37037-0. View

Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R . Fast and effective prediction of microRNA/target duplexes. RNA. 2004; 10(10):1507-17. PMC: 1370637. DOI: 10.1261/rna.5248604. View

Carthew R, Sontheimer E . Origins and Mechanisms of miRNAs and siRNAs. Cell. 2009; 136(4):642-55. PMC: 2675692. DOI: 10.1016/j.cell.2009.01.035. View

Dudekula D, Panda A, Grammatikakis I, De S, Abdelmohsen K, Gorospe M . CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol. 2015; 13(1):34-42. PMC: 4829301. DOI: 10.1080/15476286.2015.1128065. View

Ashwal-Fluss R, Meyer M, Pamudurti N, Ivanov A, Bartok O, Hanan M . circRNA biogenesis competes with pre-mRNA splicing. Mol Cell. 2014; 56(1):55-66. DOI: 10.1016/j.molcel.2014.08.019. View

10.

Ceci M, Pio G, Kuzmanovski V, Dzeroski S . Semi-Supervised Multi-View Learning for Gene Network Reconstruction. PLoS One. 2015; 10(12):e0144031. PMC: 4671612. DOI: 10.1371/journal.pone.0144031. View

11.

Li Z, Huang C, Bao C, Chen L, Lin M, Wang X . Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015; 22(3):256-64. DOI: 10.1038/nsmb.2959. View

12.

Hammond S, Bernstein E, Beach D, Hannon G . An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature. 2000; 404(6775):293-6. DOI: 10.1038/35005107. View

13.

Wang W, Yang Z, Zhang Y, Lu P, Ni Y, Sun C . Competing endogenous RNA analysis reveals the regulatory potency of circRNA_036186 in HNSCC. Int J Oncol. 2018; 53(4):1529-1543. PMC: 6086620. DOI: 10.3892/ijo.2018.4499. View

14.

Zhang Y, Liu H, Li W, Yu J, Li J, Shen Z . CircRNA_100269 is downregulated in gastric cancer and suppresses tumor cell growth by targeting miR-630. Aging (Albany NY). 2017; 9(6):1585-1594. PMC: 5509457. DOI: 10.18632/aging.101254. View

15.

Pandey P, Rout P, Das A, Gorospe M, Panda A . RPAD (RNase R treatment, polyadenylation, and poly(A)+ RNA depletion) method to isolate highly pure circular RNA. Methods. 2018; 155:41-48. PMC: 6387848. DOI: 10.1016/j.ymeth.2018.10.022. View

16.

Glazar P, Papavasileiou P, Rajewsky N . circBase: a database for circular RNAs. RNA. 2014; 20(11):1666-70. PMC: 4201819. DOI: 10.1261/rna.043687.113. View

17.

Piwecka M, Glazar P, Hernandez-Miranda L, Memczak S, Wolf S, Rybak-Wolf A . Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science. 2017; 357(6357). DOI: 10.1126/science.aam8526. View

18.

Karagkouni D, Paraskevopoulou M, Chatzopoulos S, Vlachos I, Tastsoglou S, Kanellos I . DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Res. 2017; 46(D1):D239-D245. PMC: 5753203. DOI: 10.1093/nar/gkx1141. View

19.

Wang Y, Wang Z . Efficient backsplicing produces translatable circular mRNAs. RNA. 2014; 21(2):172-9. PMC: 4338345. DOI: 10.1261/rna.048272.114. View

20.

Salzman J, Gawad C, Wang P, Lacayo N, Brown P . Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 2012; 7(2):e30733. PMC: 3270023. DOI: 10.1371/journal.pone.0030733. View