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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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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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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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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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Ribosome flow model with extended objects.

Yoram Zarai1, Michael Margaliot2, Tamir Tuller3

  • 1Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.

Journal of the Royal Society, Interface
|October 13, 2017
PubMed
Summary
This summary is machine-generated.

We introduce the ribosome flow model with extended objects (RFMEO) to better understand mRNA translation. This model reveals complex ribosome dynamics and surprising effects of ribosome footprint on protein production rates.

Keywords:
compartmental systemscontraction theoryextended objectglobal asymptotic stabilitymRNA translationsystems biology

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Area of Science:

  • Biophysics
  • Systems Biology
  • Statistical Mechanics

Background:

  • Ribosome flow models are crucial for understanding mRNA translation.
  • Existing models often lack realistic features like ribosome footprint and non-homogeneous rates.
  • Mean-field approximations are valuable but require refinement for accuracy.

Purpose of the Study:

  • To introduce and analyze the ribosome flow model with extended objects (RFMEO).
  • To compare RFMEO with the totally asymmetric simple exclusion process with extended objects (TASEPEO).
  • To investigate the impact of ribosome density, mRNA features, and transition rates on protein production.

Main Methods:

  • Developing a deterministic mechanistic model (RFMEO) for ribosome flow.
  • Utilizing systems and control theory for rigorous analysis.
  • Performing simulations to observe model behavior and steady-state dynamics.

Main Results:

  • RFMEO accurately models biophysical aspects of translation, correlating well with TASEPEO.
  • Ribosome density and protein production rate converge to unique steady states, independent of initial density.
  • Periodic transition rates lead to periodic patterns in ribosome density and production, demonstrating entrainment.

Conclusions:

  • RFMEO offers a more realistic and analytically tractable model for mRNA translation.
  • Increasing ribosome footprint can unexpectedly enhance protein production.
  • Complex ribosome density patterns can arise even with simple transition rates, complicating inference.