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Related Concept Videos

Ribosome Profiling02:24

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.
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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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: May 27, 2025

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

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Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.

Lisa Bertrand1,2, Annika Nelde3,4,5, Bertha Cecilia Ramirez1

  • 1Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190, Gif-sur-Yvette, France.

Nature Communications
|February 18, 2025
PubMed
Summary
This summary is machine-generated.

Researchers discovered 98 alternative reading frames (ARFs) in HIV-1 genomes, encoding conserved viral polypeptides. These ARF-derived peptides trigger strong T cell responses in people with HIV, offering new vaccination targets.

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Area of Science:

  • Virology
  • Genomics
  • Immunology

Background:

  • Ribosomal profiling (Riboseq) has illuminated the coding potential of genomes.
  • Understanding the full coding capacity of viral genomes is crucial for therapeutic development.

Purpose of the Study:

  • To delineate the translatome of Human Immunodeficiency Virus type 1 (HIV-1) in infected CD4+ T cells using Riboseq.
  • To identify and characterize alternative open reading frames (ARFs) and their encoded products within the HIV-1 genome.

Main Methods:

  • Ribosomal profiling (Riboseq) was employed to analyze the HIV-1 translatome.
  • Bioinformatic analysis of HIV-1 genome databases was used to assess ARF conservation.
  • T cell-based assays and mass spectrometry-based immunopeptidomics were utilized to validate ARF-encoded polypeptides and their immunogenicity.

Main Results:

  • Identification of 98 alternative open reading frames (ARFs), including small open reading frames (sORFs), across the HIV-1 genome, even in UTR regions.
  • Demonstration of conservation for most ARF amino acid sequences among HIV-1 clades B and C, with 8 ARFs showing higher conservation than overlapping canonical coding sequences (CDSs).
  • Experimental validation confirmed that ARFs encode viral polypeptides, and these ARF-derived peptides elicit potent poly-functional CD4+ and CD8+ T cell responses in individuals with HIV.

Conclusions:

  • The study expands the repertoire of conserved viral polypeptides, identifying novel targets for HIV-1 vaccination strategies.
  • The findings suggest the potential existence of previously unrecognized viral microproteins or pseudogenes encoded by ARFs.
  • ARF-derived peptides represent a significant source of T cell epitopes in HIV-1 infection.