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MirGeneDB 2.0: the metazoan microRNA complement

Fromm, Bastian, Domanska, Diana, Høye, Eirik, Ovchinnikov, Vladimir, Kang, Wenjing, Aparicio-Puerta, Ernesto, Johansen, Morten, Flatmark, Kjersti +5 more·2020·Nucleic Acids Research
DOI 10.1093/nar/gkz885PMC PMC6943042

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Abstract

Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.

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  • miRGeneDB has clearly established itself as the resource for bona fide miRNAs, while miRBase still includes scores of dubiously identified miRNAs.

    “miRGeneDB has clearly established itself as the resource for bona fide miRNAs, while miRBase still includes scores of dubiously identified miRNAs [6, 14, 16, 31, 32].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [14]

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Authors
Fromm, B., Domanska, D., Høye, E., Ovchinnikov, V., Kang, W., Aparicio-Puerta, E., Johansen, M., Flatmark, K., Mathelier, A., Hovig, E., Hackenberg, M., Friedländer, M. R., & Peterson, K. J.
Affiliations
  • Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
  • Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
  • Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
  • School of Life Sciences, Faculty of Health and Life Sciences, University of Nottingham, UK
  • Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
  • Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
  • Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2019-10-10
Volume
48
Issue
D1
Pages
D132-D141
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkz885
PMC
PMC6943042
Cited by
253
References
5
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)
Funders
  • Swedish Research Council
  • Southern and Eastern Norway Regional Health Authority (2014041, 2018014)
  • Russian Science Foundation (18-15-00098)
  • University of Nottingham
  • Norwegian Research Council
  • National Science Foundation
  • NASA-Ames
  • Dartmouth College

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