miRNA and Biogenesis

Year 2021, Volume: 10 Issue: 2, 58 - 65, 24.12.2021

Beyza Suvarıklı Alan , Mehmet Nizamlıoğlu , Zafer Bulut

https://doi.org/10.53913/aduveterinary.1008317

Abstract

The number of uncoded (non-coding; nc) RNAs with unknown functions is increasing. Since their first detections especially miRNA of ncRNAs have become very important. In fact, their importance has been well understood and their relations with diseases are more evident. It is clear that they can be used in the diagnosis of most diseases in the future. Northern hybridization, flow cytometry, cloning, qPCR, sequencing and microarray analysis can be used for miRNA detection.

Keywords

miRNA, Drosha, Dicer

References

• Agrawal, N., Dasaradhi, P.V., Mohmmed, A., Malhotra, P., Bhatnagar, R.K., & Mukherjee, S.K., (2003). RNA interference: biology, mechanism, and applications. Microbiology and Molecular Biology Reviews, 67 (4), 657-85. doi: 10.1128/MMBR.67.4.657-685.2003
• Alvarez-Garcia, I., & Miska, E.A., (2005). MicroRNA functions in animal development and human disease. Development, 132 (21), 4653-62. doi: 10.1242/dev.02073
• Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., & Tuschl, T., (2003). A uniform system for microRNA annotation. RNA, 9 (3), 277-9. doi: 10.1261/rna.2183803
• Bartel, D.P., (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116 (2), 281-97. doi: 10.1016/s0092-8674(04)00045-5
• Bartel, D.P., (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136 (2), 215-33. doi: 10.1016/j.cell.2009.01.002
• Bernstein, E., Caudy, A.A., Hammond, S.M., & Hannon, G.H., (2001). Role For A Bidentate Ribonuclease in The Initation Step of RNA Interference. Nature, 409, 363- 366. doi: 10.1038/35053110
• Betancur, J.G., & Tomari, Y., (2012). Dicer is dispensable for asymmetric RISC loading in mammals. RNA, 18 (1), 24-30. doi: 10.1261/rna.029785.111
• Betel, D., Wilson, M., Gabow, A., Marks, D.S., & Sander, C., (2007). The microRNA.org resource: targets and expression. Nucleic Acids Research, 36 (Database), 149-153. doi: 10.1093/nar/gkm995
• Cai, X., Hagedorn, C.H., & Cullen, B.R., (2004). Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA, 10 (12), 1957-66. doi: 10.1261/rna.7135204
• Carrington, J.C., & Ambros, V., (2003). Role of microRNAs in plant and animal development. Science, 301, 336–338. doi: 10.1126/science.1085242
• Carthew, R.W., & Sontheimer, E.J., (2009). Origins and Mechanisms of miRNAs and siRNAs. Cell, 136 (4), 642-55. doi: 10.1016/j.cell.2009.01.035
• Collins, R.E., & Cheng, X., (2005). Structural domains in RNAi. FEBS Letters, 579 (26), 5841-9. doi.org/10.1016/j.febslet.2005.07.072
• Court, D.L., Gan, J., Liang, Y.H., Shaw, G.X., Tropea, J.E., Costantino, N., Waugh, D.S., & Ji, X., (2013). RNase III: Genetics and function; structure and mechanism. Annual Review of Genetics, 47, 405-31. doi: 10.1146/annurev-genet-110711-155618
• Cowland, J.B., Hother, C., & Gronbaek, K., (2007). MicroRNAs and cancer. APMIS, 115 (10), 1090-106. doi: 10.1111/j.1600-0463.2007.apm_775.xml.x
• Denli, A.M., & Hannon, G.J., (2003). RNAi: an ever-growing puzzle. Trends in Biochemical Sciences, 28 (4), 196-201. doi: 10.1016/S0968-0004(03)00058-6
• Doench, J.G., Petersen, C.P., & Sharp, P.A., (2018). siRNAs can function as miRNAs. Genes & Development, 17 (4), 438–42. doi: 10.1101/gad.1064703
• Du, T., & Zamore, P.D., (2005). microPrimer: the biogenesis and function of microRNA. Development, 132 (21), 4645-52. doi.org/10.1242/dev.02070
• Dwivedi, S., Purohit, P., & Sharma, P., (2019). MicroRNAs and Diseases: Promising Biomarkers for Diagnosis and Therapeutics. Indian Journal of Clinical Biochemistry, 34 (3), 243-5. doi: 10.1007/s12291-019-00844-x
• Ghildiyal, M., & Zamore, P.D., (2009). Small silencing RNAs: an expanding universe. Nature Reviews Genetics, 10 (2), 94-108. doi: 10.1038/nrg2504
• Graves, P., & Zeng, Y., (2012). Biogenesis of Mammalian MicroRNAs: A Global View. Genomics Proteomics Bioinformatics. 10 (5), 239–245. doi: 10.1016/j.gpb.2012.06.004
• Fire, A., Xu, S.Q., Montgomery, M.K., Kostas, S.A., Driver, S.E., & Mello, C.C., (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811. doi: 10.1038/35888
• Ha, M., & Kim, V.N., (2014). Regulation of microRNA biogenesis. Nature Reviews Molecular Cell Biology, 15 (8), 509-524. doi:10.1038/nrm3838
• Hall, T.M., (2005). Structure and function of argonaute proteins. Structure, 13 (10), 1403-1408. doi: 10.1016/j.str.2005.08.005
• Han, J., Lee, Y., Yeom, K.H., Kim, Y.K., Jin, H., & Kim, V.N., (2004). The Drosha-DGCR8 complex in primary microRNA processing. Genes & Development, 18 (24), 3016-3027. doi: 10.1101/gad.1262504
• Höck, J., & Meister, G., (2008). Protein family review The Argonaute protein family. Genome Biology, 9 (2),210, doi: 10.1186/gb-2008-9-2-210
• Hutvagner, G., & Simard, M.J., (2008). Argonaute proteins: key players in RNA silencing. Nature Reviews Molecular Cell Biology, 9 (1), 22-32. doi: 10.1038/nrm2321
• Hydbring, P., & Badalian-Very, G., (2013). Clinical applications of microRNAs. F1000 Research, 6 (2), 136. doi: 10.12688/f1000research.2-136.v3
• Jansson, M.D., & Lund, A.H., (2012). MicroRNA and cancer. Molecular Oncology, 6 (6), 590-610. doi.org/10.1016/j.molonc.2012.09.006
• Jedrzejczyk, D., Gendaszewska-Darmach, E., Pawlowska, R., & Chworos, A., (2017). Designing synthetic RNA for delivery by nanoparticles. Journal of Physics: Condensed Matter, 29 (12), 123001. doi: 10.1088/1361-648X/aa5561
• Karginov, F.V., Cheloufi, S., Chong, M.M., Stark, A., Smith, A.D., & Hannon, G.J., (2010). Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Molecular Cell, 38 (6), 781-788. doi: 10.1016/j.molcel.2010.06.001
• Kim, D., & Rossi, J., (2008). RNAi mechanisms and applications. Biotechniques, 44 (5), 613-616. doi: 10.2144/000112792
• Kim, V.N., Han, J., & Siomi, M.C., (2009). Biogenesis of small RNAs in animals. Nature Reviews Molecular Cell Biology, 10 (2), 126-139. doi: 10.1038/nrm2632
• Krol, J., Loedige, I., & Filipowicz, W., (2010). The widespread regulation of microRNA biogenesis, function and decay. Nature Reviews Genetics, 11 (9), 597-610. doi: 10.1038/nrg2843
• Kwon, S.C., Nguyen, T.A., Choi, Y.G., Jo, M.H., Hohng, S., Kim, V.N., & Woo, J.S., (2016). Structure of Human DROSHA. Cell, 164 (1-2), 81-90. doi: 10.1016/j.cell.2015.12.019
• Lee, R.C., Feinbaum, R.L., & Ambros, V., (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75 (5), 843–854. doi: 10.1016/0092-8674(93)90529-y
• Lei, E.P., & Silver, P.A., (2002). Protein and RNA export from the nucleus. Developmental Cell, 2 (3), 261-272. doi.org/10.1016/S1534-5807(02)00134-X
• Lucas, K., & Raikhel, A.S., (2013). Insect microRNAs: biogenesis, expression profiling and biological functions. Insect Biochemistry and Molecular Biology, 43 (1), 24-38. doi: 10.1016/j.ibmb.2012.10.009
• MacFarlane, L., & Murphy, P.R., (2010). MicroRNA: Biogenesis, Function and Role in Cancer. Current Genomics, 11 (7), 537-561. doi: 10.2174/138920210793175895
• MacRae, I.J., Zhou, K., Li, F., Repic, A., Brooks, A.N., Cande, W.Z., Adams, P.D., & Doudna, J.A., (2006). Structural basis for double-stranded RNA processing by Dicer. Science, 311 (5758), 195-198. doi: 10.1126/science.1121638
• Macrae, I.J., Li, F., Zhou, K., Cande, W.Z., & Doudna, J.A., (2006). Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harbor Symposia on Quantitative Biology, 71 (71), 73-80. doi: 10.1101/sqb.2006.71.042
• MacRae, I.J., & Doudna, J.A., (2007). Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Current Opinion in Structural Biology, 17 (1), 138-145. doi: 10.1016/j.sbi.2006.12.002
• Mattick, J.S., & Makunin, I.V., (2006). Non-coding RNA. Human Molecular Genetics, 15 (1), 17-29. doi.org/10.1093/hmg/ddl046
• Melo, C.A., & Melo, S.A., (2013). Biogenesis and Physiology of MicroRNAs. Non-coding RNAs and Cancer, 5-24. doi: 10.1007/978-1-4614-8444-8_2
• Mortimer, S.A., Kidwell, M.A., & Doudna, J.A., (2014). Insights into RNA structure and function from genome-wide studies. Nature Reviews Genetics, 15 (7), 469-79. doi: 10.1038/nrg3681
• Napoli, C., Lemieux, C., & Jorgensen, R., (1990). Introduction of a chimeric chalcone synthase gene into Petunia result in supression of homologous revesible co-supression of homologous genes in trans. The Plant Cell, 2 (4), 279-289. doi: 10.1105/tpc.2.4.279
• Olena, A.F., & Patton, J.G., (2010). Genomic organization of microRNAs. Journal of Cellular Physiology, 222 (3), 540-545. doi: 10.1002/jcp.21993
• Pillai, R.S., (2005). MicroRNA function: multiple mechanisms for a tiny RNA?, RNA, 11 (12), 1753-1761. doi: 10.1261/rna.2248605
• Raja, M.A.G., Katas, H., & Amjad, M.W., (2019). Design, mechanism, delivery and therapeutics of canonical and Dicer-substrate siRNA. Asian Journal of Pharmaceutics Science, 14 (5), 497-510. doi.org/10.1016/j.ajps.2018.12.005
• Santosh, B., Varshney, A., & Yadava, P.K., (2014). Non-coding RNAs: biological functions and applications. Cell Biochemistry & Function, 33 (1), 14-22. doi: 10.1002/cbf.3079
• Shabalina, S.A., & Koonin, E.V., (2008). Origins and evolution of eukaryotic RNA interference. Trends Ecology Evolution, 23 (10), 578-587. doi: 10.1016/j.tree.2008.06.005
• Shukla, G.C., Singh, J., & Barik, S., (2011). MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions. Molecular and cellular pharmacology, 3 (3), 83-92. doi: 10.4255/mcpharmacol.11.13
• Singh, S.K., Pal Bhadra, M., Girschick, H.J., & Bhadra, U., (2008). MicroRNAs--micro in size but macro in function. The FEBS Journal, 275 (20), 4929-4944. doi: 10.1111/j.1742-4658.2008.06624.x
• Song, M.S., & Rossi, J.J., (2017). Molecular mechanisms of Dicer: endonuclease and enzymatic activity. Biochemical Journal, 474 (10), 1603-18. doi: 10.1042/BCJ20160759
• Tetreault, N., & De Guire, V., (2013). miRNAs: their discovery, biogenesis and mechanism of action. Clinical Biochemistry, 46 (10-11), 842-845. doi: 10.1016/j.clinbiochem.2013.02.009
• Tijsterman, M., & Plasterk, P.H., (2004). Dicers at RISC; the mechanism of RNAi, Cell, 117 (1), 1-3. doi: 10.1016/s0092-8674(04)00293-4
• Tomari, Y., & Zamore, P.D., (2018). Perspective: machines for RNAi. Genes & Development, 19 (5), 517–529. doi: 10.1101/gad.1284105
• Vermeulen, A., Behlen, L., Reynolds, A., Wolfson, A., Marshall, W.S., Karpilow, J., & Khvorova, A., (2005). The contributions of dsRNA structure to Dicer specificity and efficiency. RNA, 11 (5), 674-682. doi: 10.1261/rna.7272305
• Wahid, F., Shehzad, A., Khan, T., & Kim, Y.Y., (2010). MicroRNAs: synthesis, mechanism, function, and recent clinical trials. Biochimica et Biophysica Acta, 1803 (11), 1231-43. doi: 10.1016/j.bbamcr.2010.06.013
• Wienholds, E., & Plasterk, R.H., (2005). MicroRNA function in animal development. FEBS Letters, 579 (26), 5911-5922. doi: 10.1016/j.febslet.2005.07.070
• Williams, T., Ngo, L.H., & Wickramasinghe, V.O., (2018). Nuclear export of RNA: Different sizes, shapes and functions. Seminars in Cell and Developmental Biology, 75, 70-77. doi: 10.1016/j.semcdb.2017.08.054
• Wilson, R.C., & Doudna, J.A., (2013). Molecular mechanisms of RNA interference. Annual Review of Biophysics, 42 (1), 217-239. doi: 10.1146/annurev-biophys-083012-130404
• Wightman, B., & Ha, I.G.R., (1993). Posttranscriptional Regulation of the Heterochronic Gene lin-14 by W-4 Mediates Temporal Pattern Formation in C. elegans. Cell, 75 (5), 855-862. doi: 10.1016/0092-8674(93)90530-4
• Xu, W., Jiang, X., & Huang, L., (2019). RNA Interference Technology. In: Comprehensive Biotechnology, 560-575. doi: 10.1016/B978-0-444-64046-8.00282-2
• Zamore, P.D., Tuschl, T., Sharp, P.A, & Bartel, D.P., (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101 (1), 25-33. doi: 10.1016/S0092-8674(00)80620-0