4.3 Article

Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells

Journal

BIOLOGICAL CHEMISTRY
Volume 404, Issue 11-12, Pages 1123-1136

Publisher

WALTER DE GRUYTER GMBH
DOI: 10.1515/hsz-2023-0185

Keywords

sncRNA; molecular beacon; piRNA; live cell; imaging; fluorescence

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In this study, a small non-coding RNA called snc7SL RNA was identified and its cellular localization was determined using live cell imaging. The results showed that snc7SL RNA predominantly localizes to the nucleus, which differs from its precursor 7SL RNA in cellular localization.
Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.

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