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Imaging non-coding RNAs with Stellaris® FISH Probes

Biosearch Technologies’ Stellaris FISH (fluorescence in situ hybridization) RNA visualization method allows simultaneous detection, localization and quantification of long non-coding RNAs (lncRNA) in cells and tissues using fluorescently labeled probes. Multiple probes bind along the lncRNA to produce a cumulative signal which is imaged by fluorescence microscopy.

This imaging technology uses a simple protocol that involves fixing and permeabilizing the sample on a microscope slide, hybridizing fluorescent probes, washing away any excess probes and imaging in situ. Stellaris FISH probes can be coupled to a variety of fluorophores, including Biosearch Technologies’ CAL Fluor® and Quasar® dyes, the latter which are proprietary Cy dye analogues, to visualize multiple lncRNAs in the same cell.

These probes allow you to investigate gene regulation and visualize RNA without isolation, purification, and amplification.

Biosearch Technologies currently offers three catalogued probe sets targeting standard lncRNAs suitable for research into various aspects of nuclear lncRNAs. The standard lncRNAs are involved in different aspects of gene regulation including epigenetic silencing via retention of immature mRNAs, to organizing mRNA splicing machinery.

1. Epigenetic regulation and X-chromosome inactivation– Stellaris FISH Probes for Human XIST with Quasar 570 Dye targets the lncRNA X (inactive)-specific transcript, or XIST. XIST lncRNA-mediated chromatin regulation facilitates inactivation of one of the X chromosomes in normal female mammalian cells. The lncRNA recruits several chromatin modifying enzymes and enables the condensation of all but a few regions of the inactive X-chromosome. The number of X-clouds can also indicate the amount of X-chromosomes in partially polyploid cells such as the breast cancer cell line MCF-7.

2. Speckles and the splicing machinery depot Stellaris FISH Probes for Human MALAT1 with Quasar 570 Dye targets metastasis associated lung adenocarcinoma transcript 1 lncRNA, or MALAT1, which is another very abundant nuclear mammalian lncRNA. MALAT1 was originally discovered as a metastatic lung cancer biomarker, but has also been linked to several other human cancers. In the cells, MALAT1 is thought to organize the nuclear speckles, where components of the pre-mRNA splicing machinery can be found.

3. Paraspeckles and post-transcriptional regulation – Two sets of Stellaris FISH Probes for Human NEAT1 with Quasar 570 Dye target  the 5’ end and middle segments of the nuclear enriched autosomal transcript 1 lncRNA, or NEAT1, which is one of several lncRNAs whose expression is changed by HIV-1 infection. NEAT1 organizes the nuclear paraspeckle bodies, which are important for HIV-1 replication and late mRNA processing.

For more information on Stellaris FISH probes, visit the Stellaris FISH page at Biosearchtech.com.