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Updated: Jul 17, 2026

Single-Cell RNA Sequencing of Mutant Whole Mouse Embryos: From the Epiblast to the End of Gastrulation
Published on: June 14, 2024
Tough beginnings: alterations in the transcriptome of cloned embryos during the first two cell cycles
Rita Vassena1, Zhiming Han, Shaorong Gao
1The Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA.
Abstract:
Cloned embryos produced by somatic cell nuclear transfer (SCNT) display a plethora of phenotypic characteristics that make them different from fertilized embryos, indicating defects in the process of nuclear reprogramming by the recipient ooplasm. To elucidate the extent and timing of nuclear reprogramming, we used microarrays to analyze the transcriptome of mouse SCNT embryos during the first two cell cycles. We identified a large number of genes mis-expressed in SCNT embryos. We found that genes involved in transcription and regulation of transcription are prominent among affected genes, and thus may be particularly difficult to reprogram, and these likely cause a ripple effect that alters the transcriptome of many other functions, including oxidative phosphorylation, transport across membrane, and mRNA transport and processing. Interestingly, we also uncovered widespread alterations in the maternal (i.e., non-transcribed) mRNA population of SCNT embryos. We conclude that gene expression in early SCNT embryos is grossly abnormal, and that this is at least in part the result of incomplete reprogramming of transcription factor genes.
Insights
Somatic cell nuclear transfer (SCNT) cloned embryos show abnormal gene expression due to incomplete nuclear reprogramming. Key affected genes involve transcription, impacting various cellular functions and maternal mRNA populations.
Area of Science:
- Developmental Biology
- Reproductive Biology
- Genomics
Background:
- Somatic cell nuclear transfer (SCNT) is a technique used to create cloned embryos.
- SCNT-derived embryos often exhibit abnormal phenotypes compared to fertilized embryos.
- These abnormalities suggest defects in nuclear reprogramming by the recipient ooplasm.
Purpose of the Study:
- To investigate the extent and timing of nuclear reprogramming in SCNT embryos.
- To analyze the transcriptome of mouse SCNT embryos during early development.
Main Methods:
- Microarray analysis was employed to study gene expression.
- Transcriptome profiling was performed on SCNT embryos during the first two cell cycles.
Main Results:
- A significant number of genes were found to be mis-expressed in SCNT embryos.
- Genes regulating transcription were prominently affected, suggesting reprogramming challenges.
- Widespread alterations were observed in maternal mRNA populations.
Conclusions:
- Gene expression in early SCNT embryos is significantly abnormal.
- Incomplete reprogramming of transcription factor genes contributes to these abnormalities.
- Defects in reprogramming impact multiple cellular functions, including oxidative phosphorylation and mRNA processing.
Related Concept Videos
Cleavage and Blastulation
Reproductive Cloning
Somatic Cell Nuclear Transfer
In SCNT, an egg cell is taken from an animal and its nucleus is removed, creating an enucleated egg. Then a somatic cell—any cell that is not a sex...
Introduction to Nuclear Reprogramming
Cloning of Dolly the Sheep
Zygotic Development And Stem Cell Formation
Methods of Nuclear Reprogramming

