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Ribosome Profiling

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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: Apr 21, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Identifying (non-)coding RNAs and small peptides: challenges and opportunities.

Andrea Pauli¹, Eivind Valen, Alexander F Schier

¹Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.

Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology

|October 28, 2014

Summary

High-throughput studies reveal many novel transcripts, challenging traditional RNA classification. Ribosome profiling shows pervasive translation, uncovering functional short proteins and highlighting the importance of RNA annotation in zebrafish.

Keywords:

Apela/ELABELA/Toddler coding potential gene annotation ncRNAs peptides short ORFs zebrafish

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Last Updated: Apr 21, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Published on: February 18, 2022

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Published on: July 12, 2022

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

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Published on: September 28, 2017

Area of Science:

Genomics and Transcriptomics
Molecular Biology
Bioinformatics

Background:

High-throughput studies have identified numerous novel RNA transcripts.
The coding potential and functional roles of these transcripts remain largely uncharacterized and debated.
Previous annotation efforts may have underestimated the extent of RNA translation.

Purpose of the Study:

To review RNA annotation studies in zebrafish.
To discuss the challenges in classifying RNAs along a functional continuum.
To highlight the significance of accurate annotation for discovering novel functions.

Main Methods:

Review of existing zebrafish annotation studies.
Integration of computational approaches with ribosome profiling data.
Analysis of RNA transcripts for coding potential and functional peptide production.

Main Results:

Ribosome profiling indicates widespread translation of previously non-coding transcripts.
Discovery of novel, short functional proteins encoded by these transcripts.
Identification of transcripts where the translation process itself may confer function.

Conclusions:

Accurate RNA annotation is crucial for understanding transcript function.
The zebrafish model provides valuable insights into the RNA functional spectrum.
Discovery of novel peptides, like Apela/ELABELA/Toddler, underscores the potential of uncharacterized transcripts.