Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

4.1K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.1K
Leaky Scanning02:28

Leaky Scanning

5.6K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Nanopore-m<sup>6</sup>A-finder, a novel m<sup>6</sup>A site caller for Nanopore DRS data.

Frontiers in genetics·2026
Same author

An efficient C-to-U RNA recorder as a tool for profiling targets of RNA-binding proteins.

New biotechnology·2026
Same author

Artificial intelligence-based pathological model for pan-cancer lymph node metastasis detection: a multicentre diagnostic study with retrospective and prospective validation.

The Lancet. Digital health·2026
Same author

Accurate attenuation characterization in optical coherence tomography using multi-reference phantoms and deep learning.

Biomedical optics express·2024
Same author

Current progress in strategies to profile transcriptomic m<sup>6</sup>A modifications.

Frontiers in cell and developmental biology·2024
Same author

Expression of 5-HT Relates to Stem Cell Marker LGR5 in Patients with Gastritis and Gastric Cancer.

Digestive diseases and sciences·2022
Same journal

Enzyme conjugated magnetic nanocomposite hydrogel based on chitosan as a green fluorescent cholesterol biosensor.

International journal of biological macromolecules·2026
Same journal

A dual-responsive self-healing injectable hydrogel loaded with Isatis root-derived carbon dots toward efficient infected wound therapy.

International journal of biological macromolecules·2026
Same journal

Design strategy, functional mechanism and antibacterial applications of metal-organic framework-hyaluronic acid composite.

International journal of biological macromolecules·2026
Same journal

Dual-network gallic acid-functionalized chitosan methacryloyl/FGelMA hydrogel for diabetic wound healing via enhanced angiogenesis and inflammation modulation.

International journal of biological macromolecules·2026
Same journal

Microwave puffing synergized with deep eutectic solvent induces a wrinkled cellulose wall architecture: A new strategy for elastic and conductive wood-based piezoresistive sensors.

International journal of biological macromolecules·2026
Same journal

Macromolecular design of a bivalirudin peptide-loaded Carbopol 940 hydrogel for local thrombin inhibition and prevention of neointimal hyperplasia.

International journal of biological macromolecules·2026
See all related articles

Related Experiment Video

Updated: Jan 15, 2026

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

9.4K

A hyper-active APOBEC1 mutant boosted profiling of RNA-binding protein (RBP) targets.

Yunxiao Jia1, Chong Li1, Wei Song1

  • 1Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China.

International Journal of Biological Macromolecules
|October 6, 2025
PubMed
Summary
This summary is machine-generated.

We developed HyperSTAMP, a highly efficient tool for mapping RNA-binding protein targets in yeast. This method overcomes limitations of previous techniques, offering improved sensitivity and reliability for RBP target identification.

Keywords:
APOBEC1HyperSTAMPRNA editingRNA modificationRNA-binding protein (RBP)

More Related Videos

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

5.1K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

7.0K

Related Experiment Videos

Last Updated: Jan 15, 2026

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

9.4K
An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

5.1K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

7.0K

Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA deaminase-based tools like TRIBE and STAMP map protein-RNA interactions by detecting RNA editing events mediated by RBP-deaminase fusions.
  • The species-specific activity of deaminases has limited the broad applicability of these RNA mapping techniques.
  • STAMP, for example, has primarily been applied in mammalian systems due to these limitations.

Purpose of the Study:

  • To develop a highly efficient RNA deaminase-based tool for protein-RNA interaction mapping in Saccharomyces cerevisiae (yeast).
  • To profile the RNA targets of specific RNA-binding proteins (RBPs) in yeast using the newly developed method.
  • To compare the performance of the novel method against existing techniques in the yeast model system.

Main Methods:

  • Engineered a hyper-efficient variant of the APOBEC1 deaminase (HyperSTAMP) by introducing H122L/D124N double mutations.
  • Applied HyperSTAMP in Saccharomyces cerevisiae to map targets of RBPs BFR1 and NAB2.
  • Compared the efficiency, sensitivity, and specificity of HyperSTAMP against the original STAMP method in yeast.

Main Results:

  • HyperSTAMP demonstrated significantly higher editing efficiency and improved sequence compatibility in yeast compared to STAMP.
  • The new method exhibited excellent sensitivity, specificity, and reliability in identifying RBP targets.
  • Analysis confirmed that potential DNA editing by APOBEC1 was random and did not interfere with RBP target identification.

Conclusions:

  • The developed HyperSTAMP tool overcomes the efficiency and compatibility limitations of STAMP in non-mammalian species like yeast.
  • HyperSTAMP is a sensitive, reliable, and low-background method suitable for exploring RBP targets in yeast.
  • This advancement expands the utility of deaminase-based RNA mapping tools to a wider range of organisms.