MicroRNA nomenclature and the need for a revised naming prescription

Briefings in Functional Genomics

Volumn 15, Issue 1, 2016, Pages 65-71

  Budak, Hikmet ^a   Bulut, Reyyan ^a   Kantar, Melda ^a   Alptekin, Burcu ^a  

^a SABANCI UNIVERSITY   (Turkey)

Author keywords

Bona fide miRNAs; Canonical miRNAs; CipomiRs; isomiRNAs; microRNAs; mitomiRs

Indexed keywords

MICRORNA;

BIOGENESIS; GENE CONTROL; GENE NOMENCLATURE; HUMAN; NONHUMAN; REFERENCE DATABASE; REVIEW; GENETIC VARIATION; GENETICS; NOMENCLATURE; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; GENETIC VARIATION; HUMANS; MICRORNAS; TERMINOLOGY AS TOPIC;

EID: 84959515860     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elv026     Document Type: Review

References (35)

1. Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001;294:862-4.
2. Reinhart BJ, Weinstein EG, Rhoades MW, et al., MicroRNAs in plants. Genes Dev. 2002;16:1616-26.
3. Rhoades MW, Reinhart BJ, Lim LP, et al. Prediction of plant microRNA targets. Cell 2002;110:513-20.
4. Llave C, Kasschau KD, Rector MA, et al. Endogenous and silencing-associated small RNAs in plants. Plant Cell 2002;14:1605-19.
5. Budak H, Khan Z, Kantar M. History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress. Brief Funct Genomics 2015;14:189-98.
6. Griffiths-Jones S, The microRNA Registry. Nucleic Acids Res 2004;32:D109-11.
7. Kozomara A, Griffiths-Jones S. MiRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 2014;42:D68-73.
8. Ambros V, Bartel B, Bartel DP, et al. A uniform system for microRNA annotation. RNA 2003;9:277-9.
9. Laganà A, Paone A, Veneziano D, et al. miR-EdiTar: a database of predicted A-to-I edited miRNA target sites. Bioinformatics 2012;28:3166-8.
10. Bruno AE, Li L, Kalabus JL, et al. miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics 2012;13:44.
11. Meng Y, Shao C, Wang H, et al. Are all the miRBase-registered microRNAs true? A structure- and expression-based reexamination in plants. RNA Biol 2012;9:249-53.
12. Taylor RS, Tarver JE, Hiscock SJ, et al. Evolutionary history of plant microRNAs. Trends Plant Sci 2014;19:175-82.
13. Meyers BC, Axtell MJ, Bartel B, et al. Criteria for annotation of plant MicroRNAs. Plant Cell 2008;20:3186-90.
14. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell 2009;136:642-55.
15. Li A, Mao L. Evolution of plant microRNA gene families. Cell Res 2007;17:212-8.
16. Roberts JT, Cooper EA, Favreau CJ, et al. Continuing analysis of microRNA origins: Formation from transposable element insertions and noncoding RNA mutations. Mob Genet Elements 2013;3:e27755.
17. Son DJ, Kumar S, Takabe W, et al. The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis. Nat Commun 2013;4:3000.
18. Feng H, Wang X, Zhang Q, et al. Monodehydroascorbate reductase gene, regulated by the wheat PN-2013 miRNA, contributes to adult wheat plant resistance to stripe rust through ROS metabolism. Biochim Biophys Acta 2014;1839:1-12.
19. Van Peer G, Lefever S, Anckaert J, et al., miRBase Tracker: keeping track of microRNA annotation changes. Database (Oxford) 2014;2014:1-8.
20. Baev V, Milev I, Naydenov M, et al. Insight into small RNA abundance and expression in high- and low-temperature stress response using deep sequencing in Arabidopsis. Plant Physiol Biochem 2014;84C:105-14.
21. ZhangW, Gao S, Zhou X, et al. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 2010;11:R81.
22. Guo L, Chen F. A challenge for miRNA: Multiple isomiRs in miRNAomics. Gene 2014;544:1-7.
23. Ebhardt HA, Tsang HH, Dai DC, et al. Meta-analysis of small RNA-sequencing errors reveals ubiquitous posttranscriptional RNA modifications. Nucleic Acids Res 2009;37:2461-70.
24. JeongDH, Thatcher SR, Brown RSH, et al. Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol 2013;162:1225-45.
25. Lu S, Sun YH, Chiang VL. Adenylation of plant miRNAs. Nucleic Acids Res 2009;37:1878-85.
26. Sripada L, Tomar D, Singh R. Mitochondria: one of the destinations of miRNAs. Mitochondrion 2012;12:593-9.
27. Kamarajan BP, Sridhar J, Subramanian S. In silico prediction of microRNAs in plant mitochondria. Int J Bioautomation 2013;16:251-62.
28. Budak H, Kantar M, Bulut R, et al. Stress responsive miRNAs and isomiRs in cereals. Plant Sci 2015;235:1-13.
29. Zhang B, Wang Q. MicroRNA-based biotechnology for plant improvement. J Cell Physiol 2014;230:1-15.
30. Kurtoglu KY, Kantar M, Budak H. New wheat microRNA using whole-genome sequence. Funct Integr Genomics 2014;14:363-79.
31. Thiebaut F, Grativol C, Carnavale-Bottino M, et al. Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics 2012;13:290.
32. Xuan P, Guo M, Liu X, et al. PlantMiRNAPred: Efficient classification of real and pseudo plant pre-miRNAs. Bioinformatics 2011;27:1368-76.
33. Ha M, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 2014;15:509-24.
34. Ladewig E, Okamura K, Flynt AS, et al. Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res 2012;22:1634-45.
35. Lu C, Jeong D, Kulkarni K, et al. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). PNAS 2008;105:4951-6.