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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.
The technique helps...

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Related Experiment Video

Updated: Jun 2, 2026

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

High throughput structural analysis of yeast ribosomes using hSHAPE.

Jonathan A Leshin¹, Ryan Heselpoth, Ashton Trey Belew

¹Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.

|April 22, 2011

Summary

This summary is machine-generated.

High throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) offers a cost-effective method for mapping ribosomal RNA (rRNA) structure. This technique reveals new insights into yeast ribosome flexibility and factor binding sites.

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Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

Traditional methods for mapping ribosomal RNA (rRNA) structure are time-consuming, labor-intensive, and expensive.
Understanding rRNA structure is crucial for elucidating ribosome function and regulation.

Purpose of the Study:

To develop and apply a high-throughput, cost-effective method for global rRNA structure mapping.
To investigate the flexibility and structural organization of yeast rRNAs in intact ribosomes.

Main Methods:

Utilized high throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) with fluorescently labeled primers.
Employed capillary electrophoresis for separation of primer extension products, enabling long read lengths.
Analyzed quantitative data using SHAPEFinder software.

Main Results:

Successfully mapped the flexibility of nearly the entire sequences of the three largest rRNAs from intact, empty yeast ribosomes.
Integrated structural data with near-atomic resolution yeast ribosome structures.
Identified binding sites for known trans-acting factors and uncovered previously uncharacterized flexible rRNA regions.

Conclusions:

hSHAPE provides a powerful and economical approach for large-scale rRNA structure determination.
The findings offer new structural insights into yeast ribosome organization and factor interactions.
Further refinement of hSHAPE technology will enable dynamic mapping of rRNA structure under various functional states and conditions.