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miRSwitch: detecting microRNA arm shift and switch events

Kern, Fabian, Amand, Jeremy, Senatorov, Ilya, Isakova, Alina, Backes, Christina, Meese, Eckart, Keller, Andreas, Fehlmann, Tobias·2020·Nucleic Acids Research
DOI 10.1093/nar/gkaa323PMC PMC7319450

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Abstract

Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.

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  • Arm switching was previously thought to be strictly pathogenic in mammals.

    “a process previously thought to be strictly pathogenic in mammals (43, 45, 67).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [45]

  • The phenomena of miRNA arm switching, so far only observed in cancer, extends to healthy mammalian tissues.

    “This highlights the complexity of tissue-dependent miRNA biogenesis and indicates that the phenomena of miRNA arm switching, so far only observed in cancer, extends to healthy mammalian tissues (43–45).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [45]

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Authors
Kern, F., Amand, J., Senatorov, I., Isakova, A., Backes, C., Meese, E., Keller, A., & Fehlmann, T.
Affiliations
  • Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
  • Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
  • Department of Human Genetics, Saarland University, 66421 Homburg, Germany
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2020-05-01
Volume
48
Issue
W1
Pages
W268-W274
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkaa323
PMC
PMC7319450
Cited by
32
References
2
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)
Funders
Michael J. Fox Foundation (14446)

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