Ubiquitous Rna Targeting
Ubiquitous Rna Targeting - Related Videos
06:37
Ubiquitous and Tissue-specific RNA Targeting in Drosophila Melanogaster using CRISPR/CasRx
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Cited by 7 •
2021
This article outlines a detailed protocol for using the RNA-targeting Cas13D enzyme (RfxCas13D) in flies.
02:30
Isolation of Small Regulatory RNA–Bound Bacterial Target RNA Using Affinity Purification
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2025
Source: Mercier, N., et. al., MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria. J. Vis. Exp. (2021)This video demonstrates the isolation of MS2-tagged small regulatory RNA (sRNA) bound to its bacterial target RNA using affinity purification with a maltose-binding protein (MBP)–MS2 coat protein fusion immobilized on amylose resin.
09:36
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
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Cited by 59 •
2018
This RNA pull-down method allows identifying the RNA targets of a long non-coding RNA (lncRNA). Based on the hybridization of home-made, designed anti-sense DNA oligonucleotide probes specific to this lncRNA in an appropriately fixed tissue or cell line, it efficiently allows the capture of all RNA targets of the lncRNA.
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Cited by 15 •
2016
We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.
04:10
Helicase Activity Measurement of a Target Protein Using Biotin-Labeled RNA Duplexes
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2025
In this video, we demonstrate the procedure to determine the helicase activity of a target protein to unwind the biotin-labeled dsRNA substrate. The activity of the enzyme was identified by analyzing the electrophoretic mobility shift, followed by a chemiluminescence assay using chemiluminescent enzyme-conjugated streptavidin.
FAQs
Sequence complementarity determines which RNA molecule a guide can recognize, while the targeting platform determines what happens after binding. Antisense oligonucleotides, small interfering RNAs, and CRISPR-associated RNA-targeting systems can therefore produce different outcomes from the same general recognition principle, including transcript cleavage, degradation, translation blocking, or altered RNA processing. This distinction helps investigators match a mechanism to their experimental question.
The same targeting strategy can be examined across diverse cell types or biological contexts, but the relevant RNA may differ in abundance, localization, or biological role. These variables matter because RNA targeting is used not only to change gene expression, but also to examine how transcript distribution relates to inflammatory responses and disease outcomes. Comparing contexts can reveal whether an observed effect is broadly shared or context-dependent.
In infection research, the selected RNA determines whether the experiment focuses on a viral genome, a host immune transcript, or a broader regulatory network. Targeting viral RNA can support analysis of pathogen-associated RNA, whereas targeting host transcripts can clarify immune regulation. Keeping these target classes conceptually separate helps interpret whether a change reflects direct control of the pathogen, altered host gene expression, or both.
A practical workflow begins by identifying the RNA of interest, choosing a sequence-complementary guide format, and specifying the desired molecular outcome. The investigator then interprets the target through the mechanism available to that platform: cleavage or degradation changes RNA abundance, translation blocking limits protein production, and altered processing changes how the transcript is handled. This framework organizes experiments without treating all RNA-targeting tools as interchangeable.
Selection should follow the question being asked rather than the shared ability to bind RNA. If the goal is to reduce a transcript, cleavage or degradation is relevant; if the goal is to limit expression without describing transcript loss, translation blocking may be more informative; altered processing addresses RNA handling. The available guide type and biological context should guide the comparison.
It connects molecular RNA regulation with infection and inflammation. Investigators can examine viral genomes alongside host immune transcripts, then relate changes in RNA abundance or localization to regulatory networks and disease outcomes. This makes the approach useful for dissecting host-pathogen interactions and for informing antiviral strategy and therapeutic development, while preserving a direct focus on RNA as the controlled molecular target.