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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.6K
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

Leaky Scanning

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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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Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Viral Mutations00:36

Viral Mutations

32.4K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Related Experiment Video

Updated: Jul 14, 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

Published on: February 18, 2022

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Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling.

Shira Weingarten-Gabbay, Matthew R Bauer, Alexandra C Stanton

    Biorxiv : the Preprint Server for Biology
    |October 9, 2023
    PubMed
    Summary
    This summary is machine-generated.

    Massively Parallel Ribosome Profiling identified thousands of viral open reading frames (ORFs), including non-canonical ones. This discovery offers new vaccine targets and insights into viral gene regulation.

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    Last Updated: Jul 14, 2025

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    Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
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    Area of Science:

    • Virology
    • Genomics
    • Proteomics

    Background:

    • Understanding viral proteomes is key to viral life cycles and host interactions.
    • Existing methods have limitations in comprehensively identifying all viral open reading frames (ORFs).

    Purpose of the Study:

    • To experimentally determine the complete set of ORFs across a wide range of human-associated viral genomes.
    • To identify novel non-canonical ORFs and regulatory elements within viral genomes.

    Main Methods:

    • Development and application of Massively Parallel Ribosome Profiling (MPRP) on 20,170 designed oligonucleotides from 679 viral genomes.
    • Analysis of immunopeptidome datasets from infected cells.
    • Inspection of ribosome occupancies on viral 5' untranslated regions (UTRs) and coding sequences (CDSs).

    Main Results:

    • Identification of 5,381 ORFs, with 4,208 being non-canonical.
    • Detection of both annotated coding sequences (CDSs) and previously reported non-canonical ORFs.
    • Discovery of class I human leukocyte antigen (HLA-I) peptides derived from MPRP-identified non-canonical ORFs.
    • Identification of hundreds of upstream ORFs (uORFs) that negatively regulate canonical viral protein synthesis.

    Conclusions:

    • MPRP provides an unprecedented source of viral ORFs across diverse viral families, including highly pathogenic viruses.
    • The identified non-canonical ORFs represent potential new vaccine targets.
    • New cis-regulatory sequences within viral genomes have been exposed, enhancing our understanding of viral gene expression.