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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...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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,...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: May 13, 2026

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Spanning high-dimensional expression space using ribosome-binding site combinatorics.

Lior Zelcbuch1, Niv Antonovsky, Arren Bar-Even

  • 1Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.

Nucleic Acids Research
|March 9, 2013
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method to control protein levels for better biological system function. This approach efficiently explores gene expression to find optimal phenotypes, significantly improving yields of valuable compounds like astaxanthin.

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

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Related Experiment Videos

Last Updated: May 13, 2026

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

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

Published on: February 18, 2022

Area of Science:

  • Synthetic biology
  • Metabolic engineering
  • Systems biology

Background:

  • Precise control of protein levels is crucial for metabolic pathway function in biological systems.
  • Balancing multiple gene expression levels simultaneously presents a significant experimental challenge.

Purpose of the Study:

  • To introduce a rapid and modular method for exploring high-dimensional gene expression space.
  • To enable parallel modulation of protein abundance for optimizing biological functions.

Main Methods:

  • Combinatorially pairing genes with a set of ribosome-binding sites to modulate protein abundance.
  • Utilizing a synthetic operon with fluorescent proteins to span a 3D color space.
  • Applying the method to a recombinant carotenoid biosynthesis pathway in Escherichia coli.

Main Results:

  • Achieved modulation of protein abundance across several orders of magnitude.
  • Demonstrated spanning of a 3D color space using fluorescent proteins.
  • Revealed diverse phenotypes in a carotenoid biosynthesis pathway, with distinct accumulation profiles.
  • Increased astaxanthin yield by 4-fold compared to previous reports.

Conclusions:

  • The presented methodology offers an efficient tool for exploring high-dimensional expression spaces.
  • This approach facilitates the identification of desirable phenotypes for various applications.
  • The method has potential for optimizing industrial compound production through metabolic engineering.