The DOI matches its Crossref record; 85 of the 85 references it cites were found in a registry or an index.
Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data
Open accessAbstract
MicroRNAs (miRNAs) are ∼21-nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential posttranscriptional regulators of target mRNAs and long noncoding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of posttranscriptional regulation). Next-generation DNA sequencing methods have yielded extensive data sets of plant small RNAs, resulting in many miRNA annotations. However, it has become clear that many miRNA annotations are questionable. The sheer number of endogenous siRNAs compared with miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of "big data" from DNA sequencing. The updated criteria emphasize replication and the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.
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Cites
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Cited by
miRBase: from microRNA sequences to function
Kozomara, A., Birgaoanu, M., & Griffiths-Jones, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1141 · Cited by 4,843
MirGeneDB 2.0: the metazoan microRNA complement
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MirGeneDB 2.1: toward a complete sampling of all major animal phyla
Fromm, B., Høye, E., Domanska, D., Zhong, X., Aparicio-Puerta, E., Ovchinnikov, V., Umu, S. U., Chabot, P. J., Kang, W., Aslanzadeh, M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1101 · Cited by 147
(2023) · doi:10.1016/j.isci.2023.108740 · Cited by 1
Metadata
- Authors
- Axtell, M. J., & Meyers, B. C.
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-01-17
- Volume
- 30
- Issue
- 2
- Pages
- 272-284
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- OpenAlex
- W2949470979
- Cited by
- 429
- References
- 85
- FWCI
- 38.64
- Type
- journal article
- Language
- en
- Open access
- hybrid
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