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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
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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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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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Related Experiment Video

Updated: Oct 22, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Comprehensive evaluation of protein-coding sORFs prediction based on a random sequence strategy.

Jiafeng Yu1, Li Guo2, Xianghua Dou1

  • 1Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023 Dezhou, Shandong, China.

Frontiers in Bioscience (Landmark Edition)
|August 30, 2021
PubMed
Summary

Current methods struggle to predict protein-coding small open reading frames (sORFs) due to short sequences and low expression. This study evaluates existing tools and proposes a new strategy, highlighting the need for specialized sORF prediction methods.

Keywords:
Gene predictionGenome annotationProtein-coding geneSmall open reading framesSmall protein

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Small open reading frames (sORFs) with protein-coding potential pose annotation challenges due to short sequences and low expression.
  • Existing prediction methods for protein-coding sORFs are limited, hindered by a lack of standardized negative datasets.
  • Evaluating current sORF prediction efficiency is crucial for advancing discovery strategies.

Purpose of the Study:

  • To comprehensively evaluate mainstream methods for predicting protein-coding potential of ORFs.
  • To assess the performance of existing sORF prediction tools.
  • To propose a new prediction strategy and highlight the need for specialized tools.

Main Methods:

  • Evaluation of nine mainstream ORF prediction methods.
  • Utilizing a random sequence strategy for comprehensive assessment.
  • Development of a sequence-based prediction algorithm trained on prokaryotic sORFs.

Main Results:

  • Current prediction methods demonstrate poor performance across various sORF datasets.
  • A newly proposed sequence-based algorithm shows improved prediction capabilities.
  • The random sequence strategy proves effective for protein-coding sORF prediction.

Conclusions:

  • Protein-coding sORF discovery illuminates the 'dark proteome'.
  • There is an urgent need for specialized prediction tools for protein-coding sORFs in both eukaryotes and prokaryotes.
  • This research offers novel insights for future sORF studies.