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Ribosome Profiling

Introduction to Ribosome Profiling

Ribosome profiling is a method based on deep sequencing of ribosome-protected mRNA fragments. Purification and sequencing of these fragments provides a “snapshot” of all the ribosomes active in a cell at a specific time point. This information can determine what proteins are being actively translated in a cell.

Ribosome profiling enables systematic monitoring of cellular translation processes and prediction of protein abundance. Determining what regions of a message are being translated can help define the proteome of complex organisms. In combination with massively parallel Illumina high-throughput sequencing, ribosome profiling allows detailed and accurate in vivo analysis of protein production.

Advantages of Ribosome Profiling

Identify transcripts undergoing translation for visibility to an important aspect of gene regulation.

  • Investigate translational control and measure gene expression
  • Identify translation start sites
  • Determine rate of protein synthesis
  • Predict protein abundance

Generating Sequencing Libraries for Ribosome Profiling

Ribosome profiling uses size-exclusion chromatography. This method streamlines the steps to convert ribosome-protected RNA fragments into libraries compatible with sequencing on Illumina instruments. It is a simple, rapid, and scalable method that does not require special equipment. In contrast, other methods to isolate polysomes and monosomes rely on several hours of ultracentrifugation using either a sucrose gradient or a cushion.

Featured Products for Ribosome Profiling

NextSeq 550 System

Flexible power. Speed and simplicity for everyday genomics. 7–20 ribosome profiling samples per run.

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BaseSpace TopHat Alignment App

Aligns RNA reads and detects gene fusions using the industry-standard method. Integrated with the Cufflinks Assembly & DE App.

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Alternative to TruSeq Ribo Profile

The TruSeq Ribo Profile kits, which have been discontinued, are based on the following published protocol for ribosome profiling: Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012;7(8);1534-1550. This publication provides detailed information about the reagents required for the assay and where they can be purchased.

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Related Solutions

Cancer Research: Gene Deregulation

Sequencing ribosome-protected mRNA fragments provides critical insight into gene deregulation in cancer. By measuring the number of ribosomes engaged in translating specific mRNAs, researchers gain insight into functional changes occurring during cancer development. Learn more about cancer gene expression studies.

Complex Disease Research: Translational Regulation

Translational control determines the portion of the transcriptome that is undergoing translation. Ribosome profiling further bridges the gap between genomics/transcriptomics and proteomics, providing visibility to an important layer of post-transcriptional regulation and potential new insights into the mechanisms driving complex disease. Learn more about complex disease genomics.

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Additional Resources

RNA-Seq with the NextSeq Series
RNA-Seq with the NextSeq Series

A flexible, cost-effective solution for RNA sequencing provides a deeper understanding of biology.

RNA-Seq Data Analysis
RNA-Seq Data Analysis

User-friendly software tools simplify RNA-Seq data analysis for biologists, regardless of bioinformatics experience.

Ribosome Profiling Enables Full Translation Analysis
Ribosome Profiling Enables Full Translation Analysis

A direct method for analyzing gene expression at the protein synthesis level.

*Data calculations on file. Illumina, Inc., 2015