IsomiRage: From functional classification to differential expression of miRNA isoforms

Frontiers in Bioengineering and Biotechnology

Volumn 2, Issue SEP, 2014, Pages

  Muller, Heiko ^a   Marzi, Matteo Jacopo ^a   Nicassio, Francesco ^a  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

Alignment; Cancer; IsomiRs; miRNA; Next generation sequencing; Pipeline

Indexed keywords

ALIGNMENT; CELLS; DISEASES; PIPELINES;

BIOLOGICAL PROPERTIES; CANCER; ENZYMATIC ACTIVITIES; FUNCTIONAL CLASSIFICATION; ISOMIRS; MIRNA; NEXT-GENERATION SEQUENCING; POST-TRANSCRIPTIONAL MODIFICATION;

RNA;

EID: 84927598498     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2014.00038     Document Type: Article

References (25)

1. Ameres, S. L., and Zamore, P. D. (2013). Diversifying microRNA sequence and function. Nat. Rev. Mol. Cell Biol. 14, 475-488. doi:10.1038/nrm3611
2. Azuma-Mukai, A., Oguri, H., Mituyama, T., Qian, Z. R., Asai, K., Siomi, H., et al. (2008). Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc. Natl. Acad. Sci. U.S.A. 105, 7964-7969. doi:10.1073/pnas.0800334105
3. Bartel, D. P. (2009). microRNAs: target recognition and regulatory functions. Cell 136, 215-233. doi:10.1016/j.cell.2009.01.002
4. Burroughs, A. M., Ando, Y., De Hoon, M. J., Tomaru, Y., Nishibu, T., Ukekawa, R., et al. (2010). A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res. 20, 1398-1410. doi:10.1101/gr.106054.110
5. Cloonan, N., Wani, S., Xu, Q., Gu, J., Lea, K., Heater, S., et al. (2011). microRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol. 12, R126. doi:10.1186/gb-2011-12-12-r126
6. Ebhardt, H. A., Tsang, H. H., Dai, D. C., Liu, Y., Bostan, B., and Fahlman, R. P. (2009). Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res. 37, 2461-2470. doi:10.1093/nar/gkp093
7. Gregory, R. I., Chendrimada, T. P., Cooch, N., and Shiekhattar, R. (2005). Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123, 631-640. doi:10.1016/j.cell.2005.10.022
8. Hackenberg, M., Sturm, M., Langenberger, D., Falcon-Perez, J. M., and Aransay, A. M. (2009). miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 37, W68-W76. doi:10.1093/nar/gkp347
9. Katoh, T., Sakaguchi, Y., Miyauchi, K., Suzuki, T., Kashiwabara, S., and Baba, T. (2009). Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev. 23, 433-438. doi:10.1101/gad.1761509
10. Kawahara, Y., Zinshteyn, B., Sethupathy, P., Iizasa, H., Hatzigeorgiou, A. G., and Nishikura, K. (2007). Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315, 1137-1140. doi:10.1126/science.1138050
11. Kosaka, N., Iguchi, H., and Ochiya, T. (2010). Circulating microRNA in body fluid: a new potential biomarker for cancer diagnosis and prognosis. Cancer Sci. 101, 2087-2092. doi:10.1111/j.1349-7006.2010.01650.x
12. Krol, J., Loedige, I., and Filipowicz, W. (2010). The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet. 11, 597-610. doi:10.1038/nrg2843
13. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., et al. (2007). A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414. doi:10.1016/j.cell.2007.04.040
14. Lee, L. W., Zhang, S., Etheridge, A., Ma, L., Martin, D., Galas, D., et al. (2010). Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 16, 2170-2180. doi:10.1261/rna.2225110
15. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. doi:10.1093/bioinformatics/btp352
16. Lu, S., Sun, Y. H., and Chiang, V. L. (2009). Adenylation of plant miRNAs. Nucleic Acids Res. 37, 1878-1885. doi:10.1093/nar/gkp031
17. Neilsen, C. T., Goodall, G. J., and Bracken, C. P. (2012). IsomiRs-the overlooked repertoire in the dynamic microRNAome. Trends Genet. 28, 544-549. doi:10.1016/j.tig.2012.07.005
18. Newman, M. A., Mani, V., and Hammond, S. M. (2011). Deep sequencing of microRNA precursors reveals extensive 3' end modification. RNA 17, 1795-1803. doi:10.1261/rna.2713611
19. Pece, S., Serresi, M., Santolini, E., Capra, M., Hulleman, E., Galimberti, V., et al. (2004). Loss of negative regulation by numb over notch is relevant to human breast carcinogenesis. J. Cell Biol. 167, 215-221. doi:10.1083/jcb.200406140
20. Ramachandran, V., and Chen, X. (2008). Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321, 1490-1492. doi:10.1126/science.1163728
21. Sablok, G., Milev, I., Minkov, G., Minkov, I., Varotto, C., Yahubyan, G., et al. (2013). isomiRex: web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets. FEBS Lett. 587, 2629-2634. doi:10.1016/j.febslet.2013.06.047
22. Tan, G. C., Chan, E., Molnar, A., Sarkar, R., Alexieva, D., Isa, I. M., et al. (2014). 5' isomiR variation is of functional and evolutionary importance. Nucleic Acids Res. 42, 9424-9435. doi:10.1093/nar/gku656
23. Westholm, J. O., Ladewig, E., Okamura, K., Robine, N., and Lai, E. C. (2012). Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA 18, 177-192. doi:10.1261/rna.030627.111
24. Wheeler, B. M., Heimberg, A. M., Moy, V. N., Sperling, E. A., Holstein, T. W., Heber, S., et al. (2009). The deep evolution of metazoan microRNAs. Evol. Dev. 11, 50-68. doi:10.1111/j.1525-142X.2008.00302.x
25. Wyman, S. K., Knouf, E. C., Parkin, R. K., Fritz, B. R., Lin, D. W., Dennis, L. M., et al. (2011). Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res. 21, 1450-1461. doi:10.1101/gr.118059.110