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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Termination of Translation01:44

Termination of Translation

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...
Leaky Scanning02:28

Leaky Scanning

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 stands for...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

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RFMapp: ribosome flow model application.

Hadas Zur1, Tamir Tuller

  • 1The Blavatnik School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

Bioinformatics (Oxford, England)
|April 13, 2012
PubMed
Summary
This summary is machine-generated.

RFMapp is a new tool that estimates translation elongation rates and ribosomal density along messenger RNAs (mRNAs). This ribosome flow model (RFM) approach considers codon order and ribosome size for improved accuracy in gene analysis.

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Area of Science:

  • Computational Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Estimating translation elongation rates and ribosomal density is crucial for understanding gene expression.
  • Traditional methods often focus on mean codon translation efficiency, neglecting codon order and ribosome dynamics.

Purpose of the Study:

  • To introduce RFMapp, a graphical user interface application for efficient estimation of translation elongation rates and ribosomal density profiles along mRNAs.
  • To present an improved computational approach based on the Ribosome Flow Model (RFM) that considers codon order and ribosome characteristics.

Main Methods:

  • Developed RFMapp, a user-friendly application implementing the Ribosome Flow Model (RFM).
  • RFM incorporates codon order, ribosome size, and ribosome order in its calculations.
  • The application provides computationally efficient estimation of mRNA translation dynamics.

Main Results:

  • RFMapp enables accurate estimation of translation elongation rates.
  • The application profiles ribosomal densities along mRNAs.
  • RFM demonstrates superior performance compared to traditional predictors for both heterologous and endogenous genes.

Conclusions:

  • RFMapp offers a computationally efficient and accurate method for analyzing mRNA translation.
  • The RFM approach, by considering codon order and ribosome dynamics, provides a more comprehensive understanding of gene expression.
  • RFMapp is a valuable tool for researchers in computational and molecular biology.