Related Experiment Video
Updated: Dec 13, 2025
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Published on: April 30, 2011
Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide
Daniel Benhalevy1, Markus Hafner2
1Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA. daniel.benhalevy@nih.gov.
Abstract:
The distribution of messenger RNAs (mRNAs) to specific subcellular locations has been studied for the past two decades. Technically, studies of RNA localization are lagging those related to protein localization. Here we provide a detailed protocol for Proximity-CLIP, a method recently developed by our group, that combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA cross-linking to simultaneously profile the proteome including RNA-binding proteins (RBPs) and the RBP-bound transcriptome in any given subcellular compartment. The approach is fractionation independent and also enables studying localized RNA-processing intermediates, as well as the identification of regulatory cis-acting elements on RNAs occupied by proteins in a cellular compartment-specific manner.
More Related Videos
09:15Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
Published on: May 9, 2020
08:46Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification
Published on: May 18, 2020
Related Concept Videos
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
02:24Ribosome Profiling
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...
01:19Protein Dynamics in Living Cells
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...