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Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition

Daga, Neha and Eicher, Simone and Kannan, Abhilash and Casanova, Alain and Low, Shyan H. and Kreibich, Saskia and Andritschke, Daniel and Emmenlauer, Mario and Jenkins, Jeremy L. and Hardt, Wolf-Dietrich and Greber, Urs F. and Dehio, Christoph and von Mering, Christian. (2018) Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition. Nucleic acids research, 46 (18). pp. 9309-9320.

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Abstract

Perturbation of gene expression by means of synthetic small interfering RNAs (siRNAs) is a powerful way to uncover gene function. However, siRNA technology suffers from sequence-specific off-target effects and from limitations in knock-down efficiency. In this study, we assess a further problem: unintended effects of siRNA transfections on cellular fitness/proliferation. We show that the nucleotide compositions of siRNAs at specific positions have reproducible growth-restricting effects on mammalian cells in culture. This is likely distinct from hybridization-dependent off-target effects, since each nucleotide residue is seen to be acting independently and additively. The effect is robust and reproducible across different siRNA libraries and also across various cell lines, including human and mouse cells. Analyzing the growth inhibition patterns in correlation to the nucleotide sequence of the siRNAs allowed us to build a predictor that can estimate growth-restricting effects for any arbitrary siRNA sequence. Competition experiments with co-transfected siRNAs further suggest that the growth-restricting effects might be linked to an oversaturation of the cellular miRNA machinery, thus disrupting endogenous miRNA functions at large. We caution that competition between siRNA molecules could complicate the interpretation of double-knockdown or epistasis experiments, and potential interactions with endogenous miRNAs can be a factor when assaying cell growth or viability phenotypes.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Infection Biology > Molecular Microbiology (Dehio)
UniBasel Contributors:Dehio, Christoph
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Oxford University Press
ISSN:0305-1048
e-ISSN:1362-4962
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:02 Jul 2019 14:04
Deposited On:02 Jul 2019 14:04

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