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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.
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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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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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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 synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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SPECtre: a spectral coherence--based classifier of actively translated transcripts from ribosome profiling sequence

Sang Y Chun1, Caitlin M Rodriguez2, Peter K Todd2,3

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.

BMC Bioinformatics
|November 26, 2016
PubMed
Summary

This study introduces SPECtre, a new tool for analyzing ribosome profiling data. SPECtre accurately measures protein translation by modeling nucleotide periodicity, improving upon existing methods.

Keywords:
ClassificationRibosome profilingSpectral coherenceTranslation

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Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Ribosome profiling is a key technique for measuring active protein translation.
  • Current analytical methods for ribosome profiling have limitations in accuracy due to not fully utilizing inherent data characteristics.

Purpose of the Study:

  • To develop a novel analytical tool, SPECtre, for enhanced accuracy in ribosome profiling analysis.
  • To model tri-nucleotide periodicity of ribosomal occupancy for improved translation detection.

Main Methods:

  • Developed SPECtre software utilizing spectral coherence to analyze ribosome profiling data.
  • The tool models normalized ribosome profiling read coverage against an idealized reference signal.
  • Does not require matched mRNA-Seq data for analysis.

Main Results:

  • SPECtre demonstrates improved accuracy in detecting active translation compared to existing methods.
  • Achieves high accuracy with a low false discovery rate.
  • Shows comparable performance to other spectral coherence-based methods with reduced computational demands.

Conclusions:

  • SPECtre offers a more accurate and efficient approach to analyzing ribosome profiling data.
  • The open-source software package is readily available for researchers.
  • Represents a significant advancement in the field of translational regulation studies.