Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

Sarah Zanon Agapito-Tenfen,Terje Ingemar Traavik,Vinicius Vilperte,Rubens Onofre Nodari

doi:10.1186/s12302-018-0168-7

Abstract

BackgroundWhile some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. Furthermore, GMOs might produce naturally occurring dsRNA molecules in higher or lower quantities than its non-transgenic counterpart. This study is the first to use high-throughput technology to characterize the miRNome of commercialized GM maize events and to investigate potential alterations in miRNA regulatory networks.ResultsThirteen different conserved miRNAs were found to be dys-regulated in GM samples. The insecticide Bt GM variety had the most distinct miRNome. These miRNAs target a range of endogenous transcripts, such as transcription factors and nucleic acid binding domains, which play key molecular functions in basic genetic regulation. In addition, we have identified 20 potential novel miRNAs with target transcripts involved in lipid metabolism in maize. isomiRs were also found in 96 conserved miRNAs sequences, as well as potential transgenic miRNA sequences, which both can be a source of potential off-target effects in the plant genome. We have also provided information on technical limitations and when to carry on additional in vivo experimental testing.ConclusionsThese findings do not reveal hazards per se but show that robust and reproducible miRNA profiling technique can strengthen the assessment of risk by detecting any new intended and unintended dsRNA molecules, regardless of the outcome, at any stage of GMO development.

Highlights

While some genetically modified organisms (GMOs) are created to produce new double-stranded ribonucleic acid (RNA) molecules, in others, such molecules may occur as an unintended effect of the genetic engineering process
Deep sequencing of small RNA (sRNA) species in transgenic maize varieties In order to identify conserved maize micro RNA (miRNA) in transgenic maize varieties, sRNA libraries were constructed from leaf material and sequenced using Illumina highthroughput technology
In summary, our data revealed 13 miRNAs that may play important roles in transgenic maize plants through the dys-regulation of gene targets. These 13 miRNAs generally modulate unique gene targets but co-ordinately target a few common pathways, with partially overlapping key nodal molecules, highlighting the redundancy of miRNAs and gene targets that focuses on reprogramming critical pathways to facilitate transgene expression in maize cells

Summary

Introduction

While some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. The stability and transmissibility of dsRNAs suggest the potential for the existence of exposure routes that are relevant to environmental and human risk assessments of GM organisms [14]. In such cases, all new intended and unintended dsRNA molecules should be identified in the GM organism and products [15]. While some GMOs are intended to produce new regulatory-RNA molecules, these may arise in other GMOs not intended to express them [14, 15, 17]

Methods

Results

Discussion

Conclusion