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Cells 2018, 7(6), 54; https://doi.org/10.3390/cells7060054

Tensor Decomposition-Based Unsupervised Feature Extraction Can Identify the Universal Nature of Sequence-Nonspecific Off-Target Regulation of mRNA Mediated by MicroRNA Transfection

Department of Physics, Chuo University, Tokyo 112-8551, Japan
Received: 3 May 2018 / Revised: 28 May 2018 / Accepted: 31 May 2018 / Published: 4 June 2018
(This article belongs to the Special Issue Regulatory microRNA)
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Abstract

MicroRNA (miRNA) transfection is known to degrade target mRNAs and to decrease mRNA expression. In contrast to the notion that most of the gene expression alterations caused by miRNA transfection involve downregulation, they often involve both up- and downregulation; this phenomenon is thought to be, at least partially, mediated by sequence-nonspecific off-target effects. In this study, I used tensor decomposition-based unsupervised feature extraction to identify genes whose expression is likely to be altered by miRNA transfection. These gene sets turned out to largely overlap with one another regardless of the type of miRNA or cell lines used in the experiments. These gene sets also overlap with the gene set associated with altered expression induced by a Dicer knockout. This result suggests that the off-target effect is at least as important as the canonical function of miRNAs that suppress translation. The off-target effect is also suggested to consist of competition for the protein machinery between transfected miRNAs and miRNAs in the cell. Because the identified genes are enriched in various biological terms, these genes are likely to play critical roles in diverse biological processes.
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Keywords: tensor decomposition; miRNA transfection; sequence-nonspecific off-target regulation tensor decomposition; miRNA transfection; sequence-nonspecific off-target regulation
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Taguchi, Y.-H. Tensor Decomposition-Based Unsupervised Feature Extraction Can Identify the Universal Nature of Sequence-Nonspecific Off-Target Regulation of mRNA Mediated by MicroRNA Transfection. Cells 2018, 7, 54.

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