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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.5K
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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Leaky Scanning02:28

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Related Experiment Video

Updated: Jul 12, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

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

Published on: February 18, 2022

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Integrated workflow for discovery of microprotein-coding small open reading frames.

Kevin Cao1, Yasamin Hajy Heydary1, Gregory Tong1

  • 1Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA.

STAR Protocols
|October 24, 2023
PubMed
Summary
This summary is machine-generated.

We developed a genome-wide protocol to identify translated small open reading frame (smORF)-encoded microproteins in mammals. This method uses ribosome profiling (Ribo-seq) to find small proteins, enabling future functional studies.

Keywords:
BioinformaticsCell BiologyCell CultureGene ExpressionGenomicsMolecular BiologyRNAseqSequence AnalysisSequencing

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Area of Science:

  • Molecular Biology
  • Genomics
  • Proteomics

Background:

  • Small open reading frames (smORFs) encode microproteins, a novel class of functional biomolecules.
  • Understanding microprotein function requires identifying their translated smORFs.

Purpose of the Study:

  • To present a genome-wide protocol for identifying translated smORFs in mammalian systems.
  • To establish a foundational method for the study of microproteins.

Main Methods:

  • Generation of ribosome profiling (Ribo-seq) data.
  • In silico translation of transcriptome assembly to create an ORF database.
  • Computational analysis of Ribo-seq data to score smORF translation.

Main Results:

  • A comprehensive protocol for identifying translated smORFs across the mammalian genome.
  • Enables the discovery of novel microproteins encoded by smORFs.

Conclusions:

  • The presented protocol is crucial for the initial step in investigating microprotein functions.
  • Facilitates the expansion of the known proteome by including smORF-encoded microproteins.