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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.
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Related Experiment Video

Updated: Nov 14, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

easyCLIP analysis of RNA-protein interactions incorporating absolute quantification.

Douglas F Porter^1,2, Weili Miao^1,2, Xue Yang^1,2

¹Program in Epithelial Biology, Stanford University, Stanford, CA, USA.

Nature Communications

|March 11, 2021

Summary

Researchers developed easyCLIP, a method to quantify RNA-binding protein (RBP) interactions. This technique identifies RBPs and their target RNAs, revealing how cancer mutations affect RBP binding affinity.

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Last Updated: Nov 14, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Published on: April 30, 2011

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Published on: July 2, 2010

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

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

Published on: February 17, 2023

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Quantitative criteria for identifying RNA-binding proteins (RBPs) and their target RNAs are currently lacking.
Understanding RBP-RNA interactions is crucial for deciphering gene regulation and disease mechanisms.

Purpose of the Study:

To develop a robust method for quantifying RNA-binding protein (RBP)-RNA interactions.
To establish criteria for identifying RBPs and defining their target RNAs.
To investigate the impact of cancer-associated mutations on RBP-RNA binding.

Main Methods:

Development and application of easyCLIP (enzymatic UV cross-linking and immunoprecipitation sequencing).
Measurement of absolute cross-link rates across numerous proteins and experiments.
Statistical analysis to define thresholds for RBP identification and target RNA selection.

Main Results:

easyCLIP provides absolute cross-link rates, enhancing simplicity, efficiency, and RNA library visualization.
An RNA cross-link rate threshold was identified to distinguish RBPs from non-RBPs.
Target RNAs were defined as those with a complex frequency significantly deviating from random association.
Specific cancer mutations (KHDRBS2 R168C, A1CF E34K, PCBP1 L100P/Q) were found to increase RNA binding per RBP molecule.

Conclusions:

Quantifying RBP-RNA interactions using easyCLIP can nominate proteins as RBPs.
The method defines RBP target RNAs and assesses the impact of disease-associated mutations on RBP-RNA binding.
easyCLIP offers a powerful tool for studying RBP function and dysregulation in diseases like cancer.