Got Target? Computational Methods for MicroRNA Target Prediction and Their Extension

Overview

Journal Exp Mol Med

Specialties Biochemistry
Molecular Biology

Date 2010 Feb 24

PMID 20177143

Citations 101

Authors

Hyeyoung Min

Sungroh Yoon

Affiliations

Soon will be listed here.

Abstract

MicroRNAs (miRNAs) are a class of small RNAs of 19-23 nucleotides that regulate gene expression through target mRNA degradation or translational gene silencing. The miRNAs are reported to be involved in many biological processes, and the discovery of miRNAs has been provided great impacts on computational biology as well as traditional biology. Most miRNA-associated computational methods comprise the prediction of miRNA genes and their targets, and increasing numbers of computational algorithms and web-based resources are being developed to fulfill the need of scientists performing miRNA research. Here we summarize the rules to predict miRNA targets and introduce some computational algorithms that have been developed for miRNA target prediction and the application of the methods. In addition, the issue of target gene validation in an experimental way will be discussed.

Citing Articles

Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs.

Maji R, Schulz M Methods Mol Biol. 2024; 2883:325-341.

PMID: 39702715 DOI: 10.1007/978-1-0716-4290-0_14.

miR-1226-5p is involved in radioresistance of colorectal cancer by activating M2 macrophages through suppressing IRF1.

Choi J, Seok H, Lee D, Kwon J, Shin U, Shin I J Transl Med. 2024; 22(1):980.

PMID: 39472937 PMC: 11523791. DOI: 10.1186/s12967-024-05797-1.

Target prediction of potential candidate miRNAs from Oryza sativa to silence the Pyricularia oryzae genome in rice blast.

Suddal T, Awan M, Ali S, Sarwar M, Iqbal S, Ali Q Sci Rep. 2024; 14(1):21813.

PMID: 39294226 PMC: 11411066. DOI: 10.1038/s41598-024-72608-4.

Heart failure with preserved ejection fraction in pigs causes shifts in posttranscriptional checkpoints.

Samani S, Barlow S, Freeburg L, Catherwood G, Churillo A, Jones T Am J Physiol Heart Circ Physiol. 2024; 327(5):H1272-H1285.

PMID: 39240258 PMC: 11560071. DOI: 10.1152/ajpheart.00551.2023.

Predicting the Effect of miRNA on Gene Regulation to Foster Translational Multi-Omics Research-A Review on the Role of Super-Enhancers.

Das S, Rai S Noncoding RNA. 2024; 10(4).

PMID: 39195574 PMC: 11357235. DOI: 10.3390/ncrna10040045.

References

Lodish H, Zhou B, Liu G, Chen C . Micromanagement of the immune system by microRNAs. Nat Rev Immunol. 2008; 8(2):120-30. DOI: 10.1038/nri2252. View

John B, Enright A, Aravin A, Tuschl T, Sander C, Marks D . Human MicroRNA targets. PLoS Biol. 2004; 2(11):e363. PMC: 521178. DOI: 10.1371/journal.pbio.0020363. View

Maragkakis M, Reczko M, Simossis V, Alexiou P, Papadopoulos G, Dalamagas T . DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res. 2009; 37(Web Server issue):W273-6. PMC: 2703977. DOI: 10.1093/nar/gkp292. View

Bentwich I . Prediction and validation of microRNAs and their targets. FEBS Lett. 2005; 579(26):5904-10. DOI: 10.1016/j.febslet.2005.09.040. View

Yoon S, De Micheli G . Computational identification of microRNAs and their targets. Birth Defects Res C Embryo Today. 2006; 78(2):118-28. DOI: 10.1002/bdrc.20067. View

Addo-Quaye C, Eshoo T, Bartel D, Axtell M . Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol. 2008; 18(10):758-762. PMC: 2583427. DOI: 10.1016/j.cub.2008.04.042. View

Krek A, Grun D, Poy M, Wolf R, Rosenberg L, Epstein E . Combinatorial microRNA target predictions. Nat Genet. 2005; 37(5):495-500. DOI: 10.1038/ng1536. View

Alexiou P, Maragkakis M, Papadopoulos G, Reczko M, Hatzigeorgiou A . Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics. 2009; 25(23):3049-55. DOI: 10.1093/bioinformatics/btp565. View

Long D, Lee R, Williams P, Chan C, Ambros V, Ding Y . Potent effect of target structure on microRNA function. Nat Struct Mol Biol. 2007; 14(4):287-94. DOI: 10.1038/nsmb1226. View

10.

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

11.

Lim L, Lau N, Garrett-Engele P, Grimson A, Schelter J, Castle J . Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature. 2005; 433(7027):769-73. DOI: 10.1038/nature03315. View

12.

Grimson A, Farh K, Johnston W, Garrett-Engele P, Lim L, Bartel D . MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007; 27(1):91-105. PMC: 3800283. DOI: 10.1016/j.molcel.2007.06.017. View

13.

Kim S, Nam J, Rhee J, Lee W, Zhang B . miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics. 2006; 7:411. PMC: 1594580. DOI: 10.1186/1471-2105-7-411. View

14.

Kiriakidou M, Nelson P, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z . A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 2004; 18(10):1165-78. PMC: 415641. DOI: 10.1101/gad.1184704. View

15.

Papadopoulos G, Reczko M, Simossis V, Sethupathy P, Hatzigeorgiou A . The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res. 2008; 37(Database issue):D155-8. PMC: 2686456. DOI: 10.1093/nar/gkn809. View

16.

Wang X, El Naqa I . Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics. 2007; 24(3):325-32. DOI: 10.1093/bioinformatics/btm595. View

17.

Rajewsky N . microRNA target predictions in animals. Nat Genet. 2006; 38 Suppl:S8-13. DOI: 10.1038/ng1798. View

18.

Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E . The role of site accessibility in microRNA target recognition. Nat Genet. 2007; 39(10):1278-84. DOI: 10.1038/ng2135. View

19.

Lee R, Feinbaum R, Ambros V . The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993; 75(5):843-54. DOI: 10.1016/0092-8674(93)90529-y. View

20.

Griffiths-Jones S, Saini H, van Dongen S, Enright A . miRBase: tools for microRNA genomics. Nucleic Acids Res. 2007; 36(Database issue):D154-8. PMC: 2238936. DOI: 10.1093/nar/gkm952. View