349821 Modeling miRNA-mRNA Interactions in Breast Cancer
The MCF7 breast cancer cell line and microvesicles secreted by MCF7 cells are known to have certain microRNA (miRNA) profiles that distinguish them from other cells and the microvesicles they secrete.1 Unique features of both the cellular and microvesicular profiles include high levels of specific, natural occurring miRNAs—miR-21, let-7a, miR-100, and miR-125b—and high levels of “miRNA-like” transfer RNA (tRNA) fragments, which are even more prominent in MCF7 microvesicles. Recognizing that tRNA cleavage is a hallmark of cancer cells, the high abundance of tRNA fragments, in addition to the other miRNAs, in microvesicles has the potential of using the combination of short RNAs as a biomarker for identifying microvesicles secreted by tumor cells. The biological function of miRNAs is to modulate protein production by the translational repression of target messenger RNA (mRNA) sequences, but also by direct cleavage of the mRNA. A single miRNA can bind to many different mRNAs and multiple miRNAs can bind to one mRNA. We modeled the binding affinities of miR-21, let-7a, miR-100, miR-125b, and several tRNA fragments that have been identified experimentally1 with the mRNA for p53, a tumor suppressor, and the mRNA for Myc, which can act as an oncogene or a tumor suppressor. Thermodynamic binding affinities were computed using RNAup,2 which predicts RNA binding sites based on miRNA/tRNA and mRNA sequences and local nucleotide pair interactions. We found that the “miRNA-like” tRNA fragments exhibit significantly more favorable binding (lower ΔGbinding) to Myc mRNA than the naturally occurring miRNAs, and with much more favorable binding relative to several random mRNA sequences. We also found that three of four tRNA fragments bind more favorably to p53 mRNA than most miRNAs. Interestingly, many of the tRNA fragments bind to the same sites on p53 mRNA as the naturally occurring miRNAs, and, therefore, compete with miRNA binding to this mRNA. Moreover, the tRNA fragments in MCF7 microvesicles are more abundant compared to the miRNAs, which further enhances the competitive binding of the tRNA fragments over the miRNAs.
 Guzman, N.; Argarwal, K.; Saji, M.; Ringel, M.; Paulaitis, M. Breast cancer-specific microRNA signature unique to cell-secreted microvesicles includes “microRNA-like” transfer RNA fragments.
 Muckstein, U.; Tafer, H.; Bernhart, S.; et al. Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. SFI Working Paper (2008).
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