Subcellular Rna Separation
Subcellular Rna Separation - Related Videos
04:38
Protein Phase Separation Assay: An Optogenetic Method for Mutant RNA-Binding Protein Phase Separation in Spinal Motor Neurons of Zebrafish Larvae
0 Views •
2025
In this video, we describe a phase separation assay, wherein intracellular proteins comprising intrinsically disordered regions fused to a photosensitive oligomerization domain are induced via blue-light exposure to self-associate into membrane-less liquid-like condensates.
05:34
Denaturing Urea Polyacrylamide Gel Electrophoresis for RNA Analysis: A Technique to Separate Fluorescently Labeled Phosphorylated RNA Oligonucleotides from their Non-Phosphorylated Equivalents
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2025
In this video, we demonstrate a denaturing polyacrylamide gel electrophoresis for the separation of phosphorylated RNA species from their non-phosphorylated counterparts. The RNA species are fluorescently labeled for laser detection on the gel.
13:46
Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography
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Cited by 5 •
2011
We describe an efficient method to separate single-stranded DNA, double-stranded DNA and RNA molecules from environmental viral communities. Nucleic acids are fractionated using hydroxyapatite chromatography with increasing concentrations of phosphate-containing buffers. This method permits the isolation of all viral nucleic acid types from environmental samples.
11:19
Imaging Subcellular Structures in the Living Zebrafish Embryo
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Cited by 8 •
2016
Imaging the dynamic behavior of organelles and other subcellular structures in vivo can shed light on their function in physiological and disease conditions. Here, we present methods for genetically tagging two organelles, centrosomes and mitochondria, and imaging their dynamics in living zebrafish embryos using wide-field and confocal microscopy.
07:06
Visualizing RNA Localization in Xenopus Oocytes
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Cited by 5 •
2010
Visualization of in vivo RNA transport is accomplished by microinjection of fluorescently labeled RNA transcripts into Xenopus oocytes, followed by confocal microscopy.
FAQs
Selective lysis helps release RNA from a targeted compartment while preserving distinctions between compartments during fractionation. Subsequent centrifugation or density-based separation divides the resulting material, whereas affinity-based capture provides another route for selective recovery. These choices affect how confidently researchers can assign an RNA profile to the nucleus, cytoplasm, mitochondria, or extracellular vesicles.
Cross-contamination can blur genuine differences between cellular compartments by introducing RNA from another location. Nuclear RNA in a cytoplasmic fraction, for example, could make transcription-associated signals appear outside the nucleus. RNA degradation creates a separate problem, so careful handling and quality assessment help distinguish biological localization patterns from artifacts caused by fractionation or purification.
Comparing nuclear and cytoplasmic profiles helps separate transcriptional programs from RNA patterns associated with cytoplasmic translation. This distinction can clarify how cancer cells regulate gene expression across compartments and can reveal changes linked to tumor progression or treatment response. Including mitochondrial, noncoding, or vesicle-associated RNA extends the analysis to additional cancer-related regulatory and communication processes.
A typical workflow begins with cell fractionation, followed by selective lysis and separation using centrifugation, density-based methods, or affinity-based capture. Researchers then purify RNA from the recovered fractions and assess its quality. Maintaining controlled handling throughout this sequence is important because degradation or mixing between fractions can weaken the interpretation of compartment-specific measurements.
Centrifugation and density-based separation divide cellular material through physical fractionation, while affinity-based capture uses a selective recovery step. These approaches can therefore provide different ways to isolate or enrich material from particular compartments. The selected strategy should match the compartment being examined and the degree of separation needed for reliable RNA profiling.
Compartment-specific measurements can be used to investigate tumor progression, treatment response, and cell-state heterogeneity. They also help examine cancer communication through extracellular vesicle-associated RNA, alongside noncoding and mitochondrial RNA changes. By locating these signals within cellular or vesicular compartments, researchers can connect altered RNA patterns with distinct regulatory or communication contexts.