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Author Spotlight: A Pipeline to Analyze Lineage-Specific Mutant Embryos at Single-Cell Resolution
Published on: June 14, 2024
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Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and
Sarah E Fumagalli1, Sean Smith2, Tigran Ghazanchyan2
1Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
BMC Bioinformatics
|September 6, 2024
Summary
Mouse Embryo CoCoPUTs is a new resource detailing codon usage in mouse embryos across different tissues and stages. This data aids in understanding gene function and optimizing biotherapeutics and genetic engineering.
Area of Science:
- Developmental Biology
- Genomics
- Bioinformatics
Background:
- Mouse models are crucial for understanding mammalian embryonic development due to shared characteristics with humans.
- Integrating temporal and transcriptional data enhances knowledge of mouse embryo tissue-specific gene functions.
- Synonymous mutations can impact cell-state-specific transcriptomes and codon usage landscapes.
Purpose of the Study:
- To establish a comprehensive resource for mouse embryonic codon and codon pair usage.
- To analyze the impact of synonymous variations on tissue-specific codon usage.
- To compare mouse and human embryonic codon usage patterns.
Main Methods:
- Development of the Mouse Embryo Codon and Codon Pair Usage Tables (Mouse Embryo CoCoPUTs) resource.
- Analysis of codon, codon pair, GC, dinucleotide, and junction dinucleotide usage.
- Utilizing heatmaps for visualizing temporal usage changes and cross-species comparisons.
Main Results:
- Mouse Embryo CoCoPUTs provides detailed usage data across four strains, 15 tissue groups, 18 Theiler stages, and 26 embryonic days.
- Heatmaps revealed usage changes over time and highlighted similarities and differences between mouse and human embryonic data, particularly in the central nervous system.
- Identified potential for optimizing protein expression in biotherapeutics and tailoring gene expression in genetic engineering.
Conclusions:
- Mouse Embryo CoCoPUTs is a valuable resource for deciphering codon usage patterns in embryonic development.
- The resource offers insights into tissue-specific gene function and variation across strains and stages.
- Findings support the translation of mouse model data to human applications and advance biotherapeutic and genetic engineering development.
