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Related Concept Videos

Translation01:31

Translation

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Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life
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General Transcription Factors01:30

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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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...
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Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
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Cis-regulatory Sequences02:02

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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...
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To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
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Related Experiment Video

Updated: Jun 13, 2025

Dissection of the Auditory Bulla in Postnatal Mice: Isolation of the Middle Ear Bones and Histological Analysis
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Uncovering codon usage patterns during murine embryogenesis and tissue-specific developmental diseases.

Sarah E Fumagalli1, Sean Smith2, Brian Lin1

  • 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, United States.

Frontiers in Genetics
|June 10, 2025
PubMed
Summary

Analyzing mouse embryonic development reveals how codon usage patterns in tissue-specific genes influence developmental disorders. This research offers insights into gene regulation and disease mechanisms.

Keywords:
clustering methodsdisease-associated comparisonmachine learningmouse embryologyrelative synonymous codon usagetissue-specifictranscriptomic-weighted

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Last Updated: Jun 13, 2025

Dissection of the Auditory Bulla in Postnatal Mice: Isolation of the Middle Ear Bones and Histological Analysis
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Chromatin Immunoprecipitation Assay for Tissue-specific Genes using Early-stage Mouse Embryos
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Removal of an Internal Translational Start Site from mRNA While Retaining Expression of the Full-Length Protein
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Area of Science:

  • Developmental Biology
  • Genomics
  • Bioinformatics

Background:

  • Mouse models are crucial for understanding human genetic diseases due to shared genetic similarities.
  • Embryonic tissue-specific genes play a significant role in disease development.
  • Analyzing temporal transcriptional data can reveal insights into gene function and disease.

Purpose of the Study:

  • To analyze codon usage patterns in mouse embryonic tissues.
  • To identify how deviations in codon usage relate to developmental disorders.
  • To provide a resource for future research on embryologic disease processes.

Main Methods:

  • Analysis of transcriptomic-weighted data from four mouse strains across liver, heart, and eye tissues during embryonic development.
  • Calculation of relative synonymous codon usage (RSCU).
  • Application of dimensionality reduction and machine learning clustering techniques.

Main Results:

  • Identification of codon usage differences and similarities among mouse strains.
  • Detection of deviations in codon usage patterns between healthy and disease-linked genes.
  • Establishment of the Mouse Embryo CoCoPUTs website as a data resource.

Conclusions:

  • Codon usage patterns are critical for understanding embryonic development and associated diseases.
  • Deviations in codon usage can serve as biomarkers for developmental disorders.
  • The Mouse Embryo CoCoPUTs resource facilitates further investigation into gene regulation and disease mechanisms.