Abstract
BackgroundRapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells also vary upon irradiation. To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3′- untranslated region. We focus on the early time-course response (1 h past irradiation) to eliminate secondary mRNA expression waves.ResultsExperiments revealed that the irradiation-induced changes in the mRNA expression depend on the miRNAs which interact with mRNA. To identify the strongest interactions, we propose a mathematical model which predicts the mRNA fold expression changes, caused by perturbation of microRNA-mRNA interactions. Model was applied to experimental data including various cell lines, irradiation doses and observation times, both ours and literature-based. Comparison of modelled and experimental mRNA expression levels given miRNA level changes allows estimating how many and which miRNAs play a significant role in transcriptome response to stress conditions in different cell types. As an example, in the human melanoma cell line the comparison suggests that, globally, a major part of the irradiation-induced changes of mRNA expression can be explained by perturbed miRNA-mRNA interactions. A subset of about 30 out of a few hundred miRNAs expressed in these cells appears to account for the changes. These miRNAs play crucial roles in regulatory mechanisms observed after irradiation. In addition, these miRNAs have a higher average content of GC and a higher number of targeted transcripts, and many have been reported to play a role in the development of cancer.ConclusionsOur proposed mathematical modeling approach may be used to identify miRNAs which participate in responses of cells to ionizing radiation, and other stress factors such as extremes of temperature, exposure to toxins, and drugs.
Highlights
Rapid changes in the expression of many messenger RNA species follow exposure of cells to ionizing radiation
One of the factors regulating the expression of messenger RNA (mRNA) is degradation of transcripts mediated by miRNAs, small noncoding RNAs strongly conserved throughout evolution which, together with the proteins from the Argonaute family, function as RNA-induced silencing complexes (RISCs) [2,3,4]
The motivation for research described in this paper was provided by preliminary experimental studies, in which we examined the influence of motifs in the 3’ untranslated region (UTR) of a luciferase reporter gene, recognized by members of let-7 family, miR-21, and miR-24, on ionizing radiation-induced changes in the luciferase mRNA expression
Summary
Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells vary upon irradiation To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3′- untranslated region. Obtaining insights into the qualitative and quantitative nature of the response is complicated by superposition of potential mechanisms of primary and secondary response For this reason, we focus on the short-term transcriptional response (mostly up to 1 h past irradiation), and in particular its regulation by other RNA species. Rapid changes in the expression of many messenger RNAs (mRNAs) follow exposure of cells to irradiation by X-rays, and the change of expression of up- or down-regulated mRNAs is strongly correlated with the distribution of microRNA (miRNA) recognition motifs in their non-coding 3’-UTR sequence [1]. It is important to understand the molecular mechanisms by which miRNAs regulate mRNA levels and how the regulation is affected by stress factors
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