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Article

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

1
Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
2
Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy
3
Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
4
Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35131 Padova, Italy
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(5), 1754; https://doi.org/10.3390/ijms21051754
Received: 31 January 2020 / Revised: 26 February 2020 / Accepted: 1 March 2020 / Published: 4 March 2020
(This article belongs to the Special Issue Non-Coding RNA Biogenesis and Function)
MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function. View Full-Text
Keywords: miRNAs; moRNAs; isomiRs; isomoRs; small RNA prediction; bioinformatics; non-coding RNAs miRNAs; moRNAs; isomiRs; isomoRs; small RNA prediction; bioinformatics; non-coding RNAs
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MDPI and ACS Style

Gaffo, E.; Bortolomeazzi, M.; Bisognin, A.; Di Battista, P.; Lovisa, F.; Mussolin, L.; Bortoluzzi, S. MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data. Int. J. Mol. Sci. 2020, 21, 1754. https://doi.org/10.3390/ijms21051754

AMA Style

Gaffo E, Bortolomeazzi M, Bisognin A, Di Battista P, Lovisa F, Mussolin L, Bortoluzzi S. MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data. International Journal of Molecular Sciences. 2020; 21(5):1754. https://doi.org/10.3390/ijms21051754

Chicago/Turabian Style

Gaffo, Enrico, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, and Stefania Bortoluzzi. 2020. "MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data" International Journal of Molecular Sciences 21, no. 5: 1754. https://doi.org/10.3390/ijms21051754

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