Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Leaky Scanning02:28

Leaky Scanning

5.1K
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...
5.1K
Ribosome Profiling02:24

Ribosome Profiling

3.5K
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...
3.5K
Improving Translational Accuracy02:07

Improving Translational Accuracy

8.5K
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...
8.5K
From DNA to Protein03:06

From DNA to Protein

17.9K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
17.9K
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

22.4K
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...
22.4K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.7K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Role of Pbr1, a putative oxidoreductase, in the ER quality control and folding of yeast Fks1 glucan synthase.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Microbial characterization of oral microbiome in patients with open-angle glaucoma.

Scientific reports·2026
Same author

Anticodon loop remodeling and D-stem shape drive the specific recognition of ANN-decoding tRNAs for t6A modification.

Nucleic acids research·2026
Same author

Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in <i>Enterococcus faecalis</i>.

bioRxiv : the preprint server for biology·2026
Same author

Gel-free library preparation for next-generation RNA sequencing and small RNA quantification.

Communications biology·2026
Same author

Enterohemorrhagic <i>Escherichia coli</i> O157:H7 responds to norepinephrine gradients by tRNA reprogramming and codon-biased translation of virulence genes.

mSystems·2026

Related Experiment Video

Updated: May 27, 2025

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

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

Published on: February 18, 2022

3.5K

Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate

Evan T Davis1,2,3,4,5, Rahul Raman1,2,3, Shane R Byrne3

  • 1The RNA Institute, University at Albany, Albany, NY.

Biorxiv : the Preprint Server for Biology
|February 20, 2025
PubMed
Summary

Computational analysis of human and mouse genes reveals codon bias signatures linked to specific biological pathways. Extreme codon bias in transcription factors can regulate protein levels, impacting immune response and development.

Keywords:
Codon biasORFeomecodon re-engineeringdevelopmentgene expressionqueuosinetRNA modificationtranscription factorstranslation

More Related Videos

Using Mouse Oocytes to Assess Human Gene Function During Meiosis I
11:13

Using Mouse Oocytes to Assess Human Gene Function During Meiosis I

Published on: April 10, 2018

8.8K
Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
10:37

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Published on: May 10, 2018

12.4K

Related Experiment Videos

Last Updated: May 27, 2025

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

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

Published on: February 18, 2022

3.5K
Using Mouse Oocytes to Assess Human Gene Function During Meiosis I
11:13

Using Mouse Oocytes to Assess Human Gene Function During Meiosis I

Published on: April 10, 2018

8.8K
Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
10:37

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Published on: May 10, 2018

12.4K

Area of Science:

  • Genomics and Molecular Biology
  • Computational Biology
  • Translational Regulation

Background:

  • Codon bias, particularly involving arginine, glutamic acid, and selenocysteine, influences mRNA translation for proteins in stress responses, cell cycle, and transcriptional regulation.
  • Identifying codon bias in gene networks can uncover additional pathways under translational control.

Purpose of the Study:

  • To computationally analyze the human and mouse ORFeomes to characterize codon usage and bias across genes and biological processes.
  • To identify multi-codon bias signatures and their association with specific biological pathways and gene networks.

Main Methods:

  • Genome-wide analysis of human (19,711) and mouse (22,138) open-reading frames (ORFs).
  • Application of ORFeome-wide clustering of codon frequency data.
  • Development of codon over-use ontology mapping and hierarchical clustering.
  • Experimental re-engineering of codon usage in specific transcription factors.

Main Results:

  • ORFeome-wide clustering identified ontology-enriched biological processes, including developmental and immunological programs in both species.
  • Multi-codon bias signatures were linked to signaling, development, mitochondria, and metabolism.
  • Distinct signatures were found in human skin development/RNA metabolism and mouse olfactory transduction/ribosome pathways.
  • Extreme codon bias was observed in transcription factors and histone variants, with re-engineering impacting protein levels.

Conclusions:

  • Multi-codon bias signatures are associated with specific biological pathways.
  • Extreme codon bias in transcription factors demonstrates regulatory potential for immune response and development.
  • This study highlights species-specific translational regulation mechanisms.