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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...
Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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...
Improving Translational Accuracy02:07

Improving Translational Accuracy

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...
Improving Translational Accuracy02:07

Improving Translational Accuracy

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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Related Experiment Video

Updated: May 7, 2026

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
12:57

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Published on: December 21, 2017

Assessing gene-level translational control from ribosome profiling.

Adam B Olshen1, Andrew C Hsieh, Craig R Stumpf

  • 1Department of Epidemiology and Biostatistics, Helen Diller Family Comprehensive Cancer Center, Department of Medicine and Department of Urology, University of California, San Francisco, CA 94158, USA and Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA.

Bioinformatics (Oxford, England)
|September 20, 2013
PubMed
Summary
This summary is machine-generated.

We developed Babel, a new analytical framework to understand gene expression changes at the translation level. This method helps uncover how translational control impacts cellular functions and diseases like cancer.

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Last Updated: May 7, 2026

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Published on: December 21, 2017

Assessment of Selective mRNA Translation in Mammalian Cells by Polysome Profiling
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Assessment of Selective mRNA Translation in Mammalian Cells by Polysome Profiling

Published on: October 28, 2014

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Genomics

Background:

  • The complete picture of gene expression control across different cellular systems is not yet understood.
  • Understanding messenger RNA translation is crucial for a systems-level view of cellular molecular programs.
  • Post-transcriptional regulation's role in specific phenotypes and diseases like cancer needs further investigation.

Purpose of the Study:

  • To introduce Babel, a novel analytical framework for assessing translational regulation.
  • To enable genome-wide analysis of translation and statistically sound gene-level inference.
  • To analyze paired RNA and ribosome data for a comprehensive understanding of the translational landscape.

Main Methods:

  • Developed the Babel framework, an analytical methodology for translational regulation.
  • Employed an errors-in-variables regression model utilizing the negative binomial distribution.
  • Utilized a parametric bootstrap approach for drawing statistical inference.

Main Results:

  • Demonstrated the operating characteristics of the Babel framework using simulated data.
  • Extended prior analyses significantly by applying Babel's gene-level inference.
  • Discovered novel translationally regulated modules associated with mammalian target of rapamycin (mTOR) pathway signaling.

Conclusions:

  • Babel provides a robust methodology for analyzing genome-wide translational control.
  • The framework facilitates statistically principled inference, enhancing our understanding of gene expression regulation.
  • This approach aids in uncovering the role of translational regulation in cellular processes and disease pathogenesis.