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MirGeneDB 2.0: The metazoan microRNA complement

View ORCID ProfileBastian Fromm, Diana Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, Ernesto Aparicio-Puerta, Morten Johansen, Kjersti Flatmark, View ORCID ProfileAnthony Mathelier, View ORCID ProfileEivind Hovig, View ORCID ProfileMichael Hackenberg, View ORCID ProfileMarc R. Friedländer, Kevin J. Peterson
doi: https://doi.org/10.1101/258749
Bastian Fromm
1Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
2Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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  • For correspondence: bastianfromm@gmail.com
Diana Domanska
3Center for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
4Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Eirik Høye
2Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
5Department of Gastrointestinal and Children Surgery, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Vladimir Ovchinnikov
6School of Life Sciences, Faculty of Health and Life Sciences, University of Nottingham, United Kingdom
7Department of Human and Animal Genetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
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Wenjing Kang
1Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Ernesto Aparicio-Puerta
8Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
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Morten Johansen
3Center for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
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Kjersti Flatmark
2Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
5Department of Gastrointestinal and Children Surgery, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
9Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
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Anthony Mathelier
10Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
11Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital Radiumhospitalet, Oslo, Norway
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  • ORCID record for Anthony Mathelier
Eivind Hovig
2Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
3Center for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
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Michael Hackenberg
8Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
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Marc R. Friedländer
1Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Kevin J. Peterson
12Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, U.S.A.
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  • For correspondence: bastianfromm@gmail.com
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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 unique 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 separation 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 that represent the full taxonomic breadth of Metazoa. By consistently annotating and naming more than 10,900 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked more than 2,100 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct Metazoan evolution. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs but also biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.

Footnotes

  • This is the final version of MirGeneDB 2.0 and it has been submitted for publication. 45 species and nearly 11,000 genes in total.

  • http://mirgenedb.org/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 13, 2019.
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MirGeneDB 2.0: The metazoan microRNA complement
Bastian Fromm, Diana Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, Ernesto Aparicio-Puerta, Morten Johansen, Kjersti Flatmark, Anthony Mathelier, Eivind Hovig, Michael Hackenberg, Marc R. Friedländer, Kevin J. Peterson
bioRxiv 258749; doi: https://doi.org/10.1101/258749
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MirGeneDB 2.0: The metazoan microRNA complement
Bastian Fromm, Diana Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, Ernesto Aparicio-Puerta, Morten Johansen, Kjersti Flatmark, Anthony Mathelier, Eivind Hovig, Michael Hackenberg, Marc R. Friedländer, Kevin J. Peterson
bioRxiv 258749; doi: https://doi.org/10.1101/258749

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