Ability to form duplexes as a factor of intracellular microRNA distribution

Abstract

Background. The regulation of the content of mature microRNAs (miRNAs) in different cell compartments – the nucleus (N) and the cytoplasm (C) – makes it possible to control their availability for participation in RNA-mediated interference processes. Structurally different miRNAs, processed from different precursors (pre-miRNA), can form duplexes between molecules containing complementary sequences. The appearance of such duplexes can be considered as one of the mechanisms of miRNA activity regulation in respect to their target mRNAs. Objectives. Analysis of the miRNA distribution between nucleus and cytoplasm depending on the energy of duplex formation. Materials and methods. Data on the content of different miRNAs in the nucleus and cytoplasm in two cell lines of different origin: 5-8F of human nasopharyngeal carcinoma (NPC) and postmitotic neurons of the cerebral cortex of rat – has been used. The miRNA sequences used for analysis were taken from the miRBase database, version 22. Bioinformatic analysis of miRNA sequences for detection of molecules capable of forming miRNA duplexes and determination of their minimal free energy (MFE) of formation was carried out with the help of programs: RegRNA, version 2.0, and RNAup. Results. For the first time, a comparative analysis of the intracellular distribution N/C of different miRNAs depending on the energy of duplex formation was performed. Results of bioinformatic analysis of miRNA sequencing in 5-8F cells of human nasopharyngeal carcinoma showed that miRNAs capable of forming high-energy, i. e. more stable, duplexes, accumulate in the cytoplasm, while miRNAs forming low-energy duplexes have a larger N/C value, i. e. the level of these miRNAs is higher in the nucleus. In addition, we show that N/C distribution of miRNAs capable of forming high-energy duplexes is independent from the presence of certain short motifs, that are supposedly associated with their nuclear localization. Conclusion. The revealed enrichment of the pool of cytoplasmic miRNAs by molecules capable of forming more energetically stable duplexes may represent an additional mechanism of regulating miRNA activity in respect to their target mRNAs due to the sequestration of miRNA duplexes in the cytoplasm preventing miRNA interaction with mRNAs.