Rna Footprint Analysis
Rna Footprint Analysis - Related Videos
13:41
Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting
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Cited by 4 •
2011
This protocol describes how to quantify the Mg(II)-dependent formation of RNA tertiary structure by two methods of hydroxyl radical footprinting.
02:49
Assessing Gait by Footprint Analysis: A Method to Test Motor Coordination in Mice
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2023
In this video, we describe the footprint testing procedure and related analysis to assess gait and motor coordination in mice.
09:26
Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
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Cited by 3 •
2019
Here, we present a protocol to enrich endogenous RNA binding sites or "footprints" of RNA:protein (RNP) complexes from mammalian cells. This approach involves two immunoprecipitations of RNP subunits and is therefore dubbed RNA immunoprecipitation in tandem (RIPiT).
09:47
Spotting Cheetahs: Identifying Individuals by Their Footprints
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Cited by 25 •
2016
The cheetah (Acinonyx jubatus) is an iconic, endangered species, but conservation efforts are challenged by habitat shrinkage and conflict with commercial farmers. The footprint identification technique, a robust, accurate and cost-effective image classification system, is a new approach to monitoring cheetahs.
12:04
RNA Analysis of Environmental Samples Using RT-PCR
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2023
Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona Demonstrating Author: Bradley Schmitz Reverse transcription-polymerase chain reaction (RT-PCR) involves the same process as conventional PCR — cycling temperature to amplify nucleic acids. However, while conventional PCR only amplifies deoxyribonucleic acids (DNA), RT-PCR enables the amplification of ribonucleic acids (RNA) through the formation of complementary DNA (cDNA). This enables RNA-based organisms...
FAQs
The key signal comes from unequal cleavage across the RNA. A folded RNA complex exposes some nucleotides to the nuclease while bound proteins or other molecules shield nearby regions. Because digestion is limited rather than exhaustive, protected fragments remain available for mapping, allowing researchers to relate cleavage patterns to interaction sites and structural elements.
A change in accessibility indicates that the RNA’s interaction or structural state has changed. Regions that become more protected may gain contact with a bound molecule or adopt a less exposed configuration, whereas increased cleavage suggests greater exposure. Comparing patterns between conditions therefore helps identify rearrangements affecting regulatory sites or other functional RNA regions.
The resulting pattern can identify both potential binding sites and structural elements, but interpretation depends on the protection pattern across the RNA. A localized protected region may correspond to a contact site, while broader protection or coordinated changes may reflect folded structure. Mapping protected and unprotected segments provides the basis for distinguishing these features.
Ribosome occupancy refers to the presence of ribosomes along an RNA molecule. Protection patterns can show which RNA regions are associated with ribosomes, helping connect RNA structure and binding behavior with translation-related regulation. In genetics, this adds molecular detail to studies of how sequence regions influence gene expression through RNA-level interactions.
A typical workflow begins by forming or preserving the folded RNA complex, followed by limited nuclease digestion. Researchers then separate or identify the remaining fragments using electrophoresis, sequencing, or a related readout. Finally, they compare mapped protected regions with unprotected regions to locate interaction sites and structural features across the RNA.
Electrophoresis and sequencing are two supported ways to map the fragments that remain after digestion. Electrophoresis separates products for pattern-based comparison, while sequencing provides a mapped readout of fragment positions. Related readout methods can also be used when they preserve information about where cleavage occurred and which regions remained protected.
In genetics, the method can be applied to RNA-protein interactions, ribosome occupancy, and regulatory elements. The resulting accessibility patterns also support investigation of RNA processing, stability, localization, and translation. These applications help connect physical interactions or structural changes in RNA with mechanisms that influence how genetic information is handled after transcription.