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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...

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Related Experiment Video

Updated: Feb 20, 2026

Analysis of Translation in the Developing Mouse Brain using Polysome Profiling

Analysis of Translation in the Developing Mouse Brain using Polysome Profiling

Published on: May 22, 2021

Single-cell and isoform-specific translational profiling of the mouse brain.

Samantha L Sison¹, Federico Zampa², Eric R Kofman¹

¹Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.

|February 18, 2026

Summary

Researchers developed a new method to measure mRNA translation in single brain cells, revealing cell-type-specific patterns and isoform differences crucial for brain function and neurological disease understanding.

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Published on: November 13, 2011

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Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

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Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling |

Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling |

Published on: November 13, 2011

Area of Science:

Neuroscience
Molecular Biology
Genomics

Background:

The brain utilizes complex post-transcriptional regulation for mRNA translation.
Alternative splicing is vital for neuronal specificity and implicated in neurological disorders.
Previous methods lacked single-cell, isoform-sensitive resolution for translatome analysis.

Purpose of the Study:

To develop and apply an isoform-sensitive, single-cell translatomics platform for the brain.
To comprehensively map cell-type-specific mRNA translation in the mouse hippocampus.
To investigate differential translation of gene isoforms across distinct neuronal populations.

Main Methods:

Deployment of Surveying Ribosomal Targets by APOBEC-Mediated Profiling (Ribo-STAMP).
Integration with short-read and long-read single-cell RNA sequencing.
Analysis of mouse hippocampus translatomes at single-cell resolution.

Main Results:

Generated the first isoform-sensitive single-cell translatomes of the mouse hippocampus.
Discovered cell-type-specific translation of 3,857 alternative transcripts across 1,641 genes.
Identified differential translation of isoforms within and across 8 distinct cell types, defining translational states in CA1 and CA3 neurons.

Conclusions:

The Ribo-STAMP platform enables high-resolution mapping of cell-type and isoform-specific translation in the brain.
Findings reveal novel insights into the regulation of neuronal function and disease pathogenesis.
This technology will advance the understanding of translational control in brain physiology and neurological disorders.