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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.
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.
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Related Experiment Video

Updated: May 22, 2026

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

HEXIM1-binding elements on mRNAs identified through transcriptomic SELEX and computational screening.

Yuki Fujimoto¹, Yoshikazu Nakamura, Shoji Ohuchi

¹Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

|May 22, 2012

Summary

This summary is machine-generated.

Researchers discovered new RNA molecules, including cad mRNA, that bind to the HEXIM1 protein. This finding suggests HEXIM1 may regulate specific gene expressions by interacting with these RNAs.

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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

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

Published on: July 2, 2010

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Last Updated: May 22, 2026

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

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

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

Published on: July 2, 2010

Area of Science:

Molecular Biology
Gene Regulation
RNA-Protein Interactions

Background:

Positive transcription elongation factor b (P-TEFb) is a key regulator of RNA polymerase II (RNAPII)-mediated transcription.
P-TEFb activity is inhibited by the RNA-binding protein HEXIM1, typically in complex with 7SK snRNA.
The precise mechanisms and additional binding partners of HEXIM1 in gene regulation are not fully understood.

Purpose of the Study:

To identify novel cellular RNAs that interact with the HEXIM1 protein.
To investigate the functional implications of HEXIM1-RNA interactions in gene expression regulation.

Main Methods:

Systematic evolution of ligands by exponential enrichment (SELEX) was employed using a HeLa cDNA library to discover HEXIM1-binding RNAs.
In vitro mutational analysis was performed to pinpoint the binding site of cad mRNA on HEXIM1.
Co-immunoprecipitation assays and computational searches were utilized to validate and identify other potential HEXIM1-binding RNAs.

Main Results:

Cadmium (cad) mRNA was identified as a novel HEXIM1-binding RNA, with binding confirmed in HeLa cells.
The interaction between cad mRNA and HEXIM1 involves a bulged stem structure within exon 11 of the mRNA.
Brd4 and Tcf3 mRNAs, possessing similar stem structures, were also found to be co-immunoprecipitable with HEXIM1.

Conclusions:

HEXIM1 interacts with specific mRNAs, including cad, brd4, and tcf3, through distinct RNA structural motifs.
These findings suggest a broader role for HEXIM1 beyond its known interaction with 7SK snRNA.
HEXIM1 may function as a regulator of specific gene expressions by binding to these identified mRNAs.