Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Ribosome Profiling

Ribosome Profiling

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...

Regulated mRNA Transport

Regulated mRNA Transport

In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...

You might also read

Related Articles

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

Sort by

Same author

Nano-engineered Ag@MgO embedded chitosan hydrogel patch for potent antibacterial activity, antibiofilm activity, and infected wound healing.

Journal of materials chemistry. B·2026

Same author

Exploring Combination Therapy for the Management of Psychotic Disorders: A Comprehensive Review.

Current pharmaceutical design·2026

Same author

MSML-DenseXmer: harnessing vision transformers through integration with novel dense networks for medical image fusion.

Scientific reports·2026

Same author

Influence of chronic hyperglycemia on corneal endothelium structural integrity with emphasis on hexagonality.

International ophthalmology·2026

Same author

Peripheral complement C4 protein in schizophrenia: Association with gene copy number and immune cell subtypes.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Artificial Intelligence-Enhanced Electrocardiography and Health Records to Predict Cardiac Arrest.

JACC. Advances·2026

Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026

Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026

Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026

Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026

Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026

Same journal

Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants.

Nature protocols·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 4, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.

Surbhi Sharma^1,2, Madeline E Rasband^1,2, Xuemei Wang^1,2

¹Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.

Nature Protocols

|April 2, 2026

Summary

This summary is machine-generated.

Researchers developed APEX sequencing (APEX-seq) to map RNA locations within cells. This proximity labeling method reveals the RNA repertoire at specific subcellular locations, advancing our understanding of RNA biology.

More Related Videos

TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

Published on: September 10, 2015

Visualizing RNA Localization in Xenopus Oocytes

Visualizing RNA Localization in Xenopus Oocytes

Published on: January 14, 2010

Related Experiment Videos

Last Updated: Apr 4, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

Published on: September 10, 2015

Visualizing RNA Localization in Xenopus Oocytes

Visualizing RNA Localization in Xenopus Oocytes

Published on: January 14, 2010

Area of Science:

Cell Biology
Molecular Biology
Genomics

Background:

Protein localization is well-understood, but RNA subcellular localization remains largely unknown.
RNA localization is critical for gene expression regulation, influencing RNA fate and function.
Studying RNA in specific organelles, especially membrane-bound and membrane-less ones, is challenging due to limited tools.

Purpose of the Study:

To introduce a scalable method for determining RNA subcellular localization in native cellular environments.
To provide a detailed protocol for APEX sequencing (APEX-seq) applicable to diverse subcellular locations.
To enable unbiased discovery of RNA localization and associated regulatory mechanisms.

Main Methods:

APEX sequencing (APEX-seq) utilizes an engineered ascorbate peroxidase (APEX2) fused to a protein of interest.
APEX2 catalyzes proximity-dependent biotinylation of RNAs in its vicinity upon addition of biotin-phenol and hydrogen peroxide.
Biotinylated RNAs are captured using streptavidin beads, followed by sequencing to identify the localized RNA transcriptome.

Main Results:

APEX-seq provides transcriptome-wide information on RNA subcellular addresses.
The protocol is adaptable to various subcellular locations, including organelles and condensates.
The entire workflow, from labeling to data analysis, can be completed within one week with established cell lines.

Conclusions:

APEX-seq offers a powerful, unbiased approach to map RNA localization across the cell.
This method facilitates the discovery of novel RNA-organelle interactions.
APEX-seq can generate hypotheses for RNA localization mechanisms and regulatory pathways.