Changes in nuclear and cytoplasmic microRNA distribution following hypoxic stress

Purpose: MicroRNAs have well characterized roles in cytoplasmic gene regulation by binding mRNA and inhibiting translation. However, besides this post-transcriptional gene silencing, miRNAs have also been implicated in transcriptional gene regulation and alternative splicing, events that are restricted to the cell nucleus. The nuclear functions of miRNAs are currently not understood, and there is a paucity of systematic studies of miRNA nuclear-cytoplasmic distribution and fewer still which have investigated this in the context of physiological conditions. Methods: Here we performed nuclear-cytoplasmic fractionation in a mouse endothelial cell line in hypoxia and characterized the localization of miRNAs using small RNA sequencing. Results: We show here that there is a broad population of mature miRNAs in the cell nucleus and that it is also altered upon exposure to hypoxia. Conclusions: Our results strongly imply that miRNAs have extensive regulatory functions in the nucleus and expand potential therapeutic use of small RNA molecules. Overall design: C166 endothelial cells were treated with hypoxia (NT, 2h and 24h timepoints) and fractionated into nuclear and cytoplasmic samples that were used for sequencing. Samples were done in duplicates.