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Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [single cell ATAC-seq]

ABSTRACT: Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [single cell ATAC-seq]

PROVIDER: PRJNA991644 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR25153800_1.fastq.gz	Fastqsanger.gz
	SRR25153800_2.fastq.gz	Fastqsanger.gz
	SRR25153900_1.fastq.gz	Fastqsanger.gz
	SRR25153900_2.fastq.gz	Fastqsanger.gz

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Project description:Somatic cell nuclear transfer and transcription factor overexpression can induce reprogramming of somatic cells, whereby one cell fate is changed into another cell fate of choice. Yet the efficiency of this process for generating functional cells is low, limiting their therapeutic applications. The persistence of transcriptional memory from the cell's prior identity is thought to be a major hindrance to effective reprogramming and differentiation to functional cell types. To explore the effects of transcriptional memory on cell fate specification of reprogrammed cells, we analyzed epidermal tissue development in nuclear transfer embryos derived from endoderm nuclei. Our findings reveal variations in the success rate of differentiation to functional cells across cell types in cloned embryos. While some cell types, such as goblet cells, differentiated normally, a specific subset of cells resisted cell fate reprogramming, adopting a new endoderm-like state and disrupting normal body patterning. Furthermore, inefficient transcriptional reprogramming correlated with reduced basal stem cell populations, faulty differentiation of basal stem cell-derived fates, and increased cell death in the epidermis of cloned embryos. Crucially, we identified that the memory of active transcriptional states linked to key endoderm transcription factors plays a significant role in these issues. Mimicking active state transcriptional memory of these genes through the forced expression of Sox17b and Foxa4 in the epidermis of fertilized embryos produced the same defects. On the contrary, reducing transcriptional memory by interfering with the expression of Sox17b led to the rescue of observed epidermal defects. In summary, our study suggests that transcriptional memory tends to persist predominantly in specific reprogrammed cell types, hindering their differentiation into functional cells and embryonic structures. This underscores the critical need to assess and reduce transcriptional memory from the previous somatic identity during reprogramming, to efficiently generate functional cell types for therapeutic applications.

Dataset Information

Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [single cell ATAC-seq]

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