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Molecules 2018, 23(6), 1367; https://doi.org/10.3390/molecules23061367

Discovering Structural Motifs in miRNA Precursors from the Viridiplantae Kingdom

1
Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
2
Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
*
Author to whom correspondence should be addressed.
Received: 29 April 2018 / Revised: 1 June 2018 / Accepted: 4 June 2018 / Published: 6 June 2018
(This article belongs to the Special Issue Molecular Computing and Bioinformatics)
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Abstract

A small non-coding molecule of microRNA (19–24 nt) controls almost every biological process, including cellular and physiological, of various organisms’ lives. The amount of microRNA (miRNA) produced within an organism is highly correlated to the organism’s key processes, and determines whether the system works properly or not. A crucial factor in plant biogenesis of miRNA is the Dicer Like 1 (DCL1) enzyme. Its responsibility is to perform the cleavages in the miRNA maturation process. Despite everything we already know about the last phase of plant miRNA creation, recognition of miRNA by DCL1 in pre-miRNA structures of plants remains an enigma. Herein, we present a bioinformatic procedure we have followed to discover structure patterns that could guide DCL1 to perform a cleavage in front of or behind an miRNA:miRNA* duplex. The patterns in the closest vicinity of microRNA are searched, within pre-miRNA sequences, as well as secondary and tertiary structures. The dataset consists of structures of plant pre-miRNA from the Viridiplantae kingdom. The results confirm our previous observations based on Arabidopsis thaliana precursor analysis. Hereby, our hypothesis was tested on pre-miRNAs, collected from the miRBase database to show secondary structure patterns of small symmetric internal loops 1-1 and 2-2 at a 1–10 nt distance from the miRNA:miRNA* duplex. View Full-Text
Keywords: miRNA biogenesis; structural patterns; DCL1 miRNA biogenesis; structural patterns; DCL1
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Miskiewicz, J.; Szachniuk, M. Discovering Structural Motifs in miRNA Precursors from the Viridiplantae Kingdom. Molecules 2018, 23, 1367.

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