Publication: Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism


Agapito-Tenfen, S.Z., Vilperte, V., Traavik, T.I., Nodari, R. (2018) Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism. Environmental Sciences Europe,

The genetically modified organisms we have been cultivating worldwide have been mostly created to produce a new insecticide protein or an enzyme to overcome the toxicity of herbicide sprays. New developments in genetic engineering technology have now created GM crops that have intentionally altered RNA contend. These new crops produce novel double-stranded RNA (dsRNA) molecules that cross the plant cell barrier and affect the herbivore insects that eats them.

Exposure to dsRNA can trigger a process called RNA interference (RNAi). RNAi is a gene regulation process by which the production of certain proteins is disrupted when dsRNA molecules interact with the DNA sequence of that gene or when there is a decrease in protein expression through the down-regulation of endogenous or exogenous mRNA by the interaction of small RNAs molecules (siRNAs or microRNAs – miRNAs) with catalytic RNA-induced silencing complex (RISC) to bind to homologous mRNA sequences and to cleave/break them. Such small double-stranded RNAs are known to control a wide range of biological processes in eukaryotic organisms, from embryogenesis, to developmental and cellular behaviour, and response to biotic and abiotic stress.

Crop breeders have now applied this knowledge to engineer GM plants that produce new transgenic dsRNA molecules that interact with vital proteins inside herbivores to kill them. However, the contend of such small double-stranded RNA molecules might be also altered in currently commercialized GM crops as an unintended result of the genetic engineering process.

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. Unless the GM plant is intended to produce new dsRNA molecules, the RNA contend is rarely formally considered in a risk assessment. This is surprising since many GMO risk assessment guidance draw special attention to the characterization of novel RNAs, frequently mentioning the need to provide information on any expressed substances in the recombinant-DNA plant.

Thirteen 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 vivoexperimental testing. These findings do not reveal hazards per sebut 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.