MicroRNAs and reactive oxygen species: are they in the same regulatory circuit?

Interactions of living organisms with their environment mainly involve modulation of gene expression by stimulation or silencing. One of the epigenetic mechanisms that regulate translation and the levels of transcripts is RNA interference, in which microRNAs (miRNAs) address RNA-induced silencing complexes (RISCs) to degrade specific mRNAs or to silence their translation. In this mechanism, double stranded RNA structure is crucial for miRNA biogenesis and the action of RISCs. RNA molecules can be modified structurally by reactive oxygen and nitrogen species (ROS and RNS) that are produced in cells of all aerobic organisms and may be induced by environmental factors. Here we describe experiments in which changes of ROS and transcript levels are induced by X-irradiation and measured using flow cytometer and the fluorescent dye 2',7'-dichlorofluorescein diacetate and microarray methods in cultured human K562, Me45 and HCT116 cells. Analysis of the nucleotide sequences of mRNAs which are up- or down-regulated after irradiation shows significant differences in the distributions of miRNA-targeted motives between these two groups. Immediately after irradiation most miRNAs behave as "up-regulators", showing more targets in up-than in down-regulated transcripts, and this changes about 12h later when we also observe changes in ROS and miRNA levels. Our results suggest that the changes in the transcriptome could result from changes in RNA interference and that these effects could be related to the changed ROS levels in irradiated cells. We propose that such modulation of gene expression at the mRNA level may be implicated more generally in cellular responses to stresses where ROS levels change.