Abstract
microRNA capture affinity technology (miR-CATCH) uses affinity capture biotinylated antisense oligonucleotides to co-purify a target transcript together with all its endogenously bound miRNAs. The miR-CATCH assay is performed to investigate miRNAs bound to a specific mRNA. This method allows to have a total vision of miRNAs bound not only to the 3′UTR but also to the 5′UTR and Coding Region of target messenger RNAs (mRNAs).
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References
Jin Y, Chen Z, Liu X, Zhou X (2013) Evaluating the MicroRNA targeting sites by luciferase reporter gene assay. Methods Mol Biol 936:117–127
Denti MA, Rosa A, Sthandier O, De Angelis FG, Bozzoni I (2004) A new vector, based on the polII promoter of the U1 snRNA gene, for the expression of siRNAs in mammalian cells. Molecular Ther 10:191–199
Obad S, dos Santos CO, Petri A, Heidenblad M, Broom O, Ruse C, Fu C, Lindow M, Stenvang J, Straarup EM, Hansen HF, Koch T, Pappin D, Hannon GJ, Kauppinen S (2011) Silencing of microRNAs families by seed-targeting tiny LNAs. Nat Genet 43:371–378
Li P, Chen Y, Juma CA, Yang C, Huang J, Zhang X, Zeng Y (2019) Differential inhibition of target gene expression by human microRNAs. Cell 8:791
Hassan T, Smith SGJ, Gaughan K, Oglesby IK, O’Neill S, McElvaney NG, Greene CM (2013) Isolation and identification of cell-specific microRNAs targeting a messenger RNA using a biotinylated antisense oligonucleotide capture affinity technique. Nucleic Acids Res 41:e71
Vencken S, Hassan T, McElvaney NG, Smith SGJ, Greene CM (2015) miR-CATCH: microRNA capture affinity technology. In: Sioud M (ed) RNA interference: challenges and therapeutic opportunities, methods in molecular biology, vol 1218. Springer, Heidelberg, pp 365–373
Piscopo P, Grasso M, Fontana F, Crestini A, Puopolo M, Del Vescovo V, Venerosi A, Calamandrei G, Vencken SF, Greene CM, Confaloni A, Denti MA (2016) Reduced miR-659-3p levels correlate with progranulin increase in hypoxic conditions: implications for frontotemporal dementia. Front Mol Neurosci 9:31. https://doi.org/10.3389/fnmol.2016.00031
Palfi A, Hokamp K, Hauck SM, Vencken S, Millington-Ward S, Chadderton N, Carrigan M, Kortvely E, Greene CM, Kenna PF, Farrar GJ (2016) microRNA regulatory circuits in a mouse model of inherited retinal degeneration. Sci Rep 6:31431. https://doi.org/10.1038/srep31431
De Santi C, Vencken S, Blake J, Haase B, Benes V, Gemignani F, Landi S, Greene CM (2017) Identification ofMiR-21-5p as a functional regulator of MesothelinExpression using MicroRNA capture AffinityCoupled with next generation sequencing. PLoS One 12:e0170999. https://doi.org/10.1371/journal.pone.0170999
Griffith A, Kelly PS, Vencken S, Lao NT, Greene CM, Clynes M, Barron N (2018) miR-CATCH identifies biologically active miRNA regulators of the pro-survival gene XIAP, in Chinese hamster ovary cells. Biotechnol J 13:e1700299. https://doi.org/10.1002/biot.201700299
Ragusa M, Barbagallo D, Chioccarelli T, Manfrevola F, Cobellis G, Di Pietro C, Brex D, Battaglia R, Fasano S, Ferraro B, Sellitto C, Ambrosino C, Roberto L, Purrello M, Pierantoni R, Chianese R (2019) CircNAPEPLD is expressed in human and murine spermatozoa and physically interacts with oocyte miRNAs. RNA Biol 16:1237–1248. https://doi.org/10.1080/15476286.2019.1624469
Marranci A, D’Aurizio R, Vencken S, Mero S, Guzzolino E, Rizzo M, Pitto L, Pellegrini M, Chiorino G, Greene CM, PolisenoL (2019) Systematic evaluation of the microRNAome through miR-CATCHv2.0identifies positive and negative regulators of BRAF-X1 mRNA. RNA Biol 16:865–878. https://doi.org/10.1080/15476286.2019.1600934
Precazzini F, Detassis S, Imperatori AS, Denti MA, Campomenosi P (2021) Measurement methods for the development of microRNA-based tests for cancer diagnosis. Int J Mol Sci 21:1176
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415. https://doi.org/10.1093/nar/gkg595
Okonechnikov K, Golosova O, Fursov M, the UGENE team (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167. https://doi.org/10.1093/bioinformatics/bts091
Altschul SF, GishW MW, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Sugimoto N, Nakano M, Nakano S (2000) Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry 39:11270–11281. https://doi.org/10.1021/bi000819p
Acknowledgments
We wish to thank Catherine M. Greene (Royal College of Surgeons in Ireland, Dublin) for having hosted Francesca Fontana in her laboratory in the Fall of 2013, and Sebastian Vencken (Royal College of Surgeons in Ireland, Dublin) for having taught Francesca the miR-CATCH protocol. We also wish to thank Francesca Fontana for having shared with the rest of the Denti Lab her knowledge of the miR-CATCH methodology.
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Zeni, A., Grasso, M., Denti, M.A. (2022). Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH). In: Dassi, E. (eds) Post-Transcriptional Gene Regulation. Methods in Molecular Biology, vol 2404. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1851-6_11
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DOI: https://doi.org/10.1007/978-1-0716-1851-6_11
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