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Related Concept Videos

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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Ribosome Profiling02:24

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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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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Directing Proteins to the Rough Endoplasmic Reticulum01:34

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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Initiation of Translation02:33

Initiation of Translation

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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
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Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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Updated: Sep 15, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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An expanded reference catalog of translated open reading frames for biomedical research.

Sonia Chothani, Jorge Ruiz-Orera, Jack A S Tierney

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    |July 17, 2025
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    Summary

    This study expands the catalog of human non-canonical open reading frames (ncORFs), identifying 28,359 ncORFs. A subset of 7,888 ncORFs shows translation evidence comparable to canonical genes, providing a high-quality resource for research.

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    Area of Science:

    • Genomics
    • Proteomics
    • Bioinformatics

    Background:

    • Non-canonical open reading frames (ncORFs) were previously omitted from genome annotations, hindering biomedical research.
    • The initial 2022 catalog of human ncORFs lacked a standardized framework for assessing translation evidence.

    Purpose of the Study:

    • To present an expanded and refined catalog of human ncORFs.
    • To establish a data-driven framework for evaluating translation evidence in ncORFs.
    • To provide a high-quality, reliable reference set of ncORFs for downstream research.

    Main Methods:

    • Incorporated additional datasets and relaxed constraints on ORF length and start-codon.
    • Developed a translation signature score framework to quantify evidence of translation.
    • Defined a 'Primary set' of ncORFs with robust translation signals.

    Main Results:

    • Identified a comprehensive set of 28,359 ncORFs, nearly four times larger than the previous catalog.
    • Derived a 'Primary set' of 7,888 ncORFs with translation evidence comparable to canonical protein-coding genes.
    • Established a standardized framework for assessing ncORF translation evidence.

    Conclusions:

    • The updated ncORF catalog is significantly expanded and refined, enhancing its utility for biomedical research.
    • The 'Primary set' offers a reliable, high-quality resource for studies requiring strong ncORF translation evidence.
    • This community-driven effort makes ncORFs more accessible and actionable for the research community.