Molecular characterization of bovine embryonic stem cells derived from IVF, cloned, and parthenogenetic embryos
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA718333 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14097638.fastq.gz | Fastqsanger.gz | |||
| SRR14097639_1.fastq.gz | Fastqsanger.gz | |||
| SRR14097639_2.fastq.gz | Fastqsanger.gz | |||
| SRR14097640_1.fastq.gz | Fastqsanger.gz | |||
| SRR14097640_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Embryonic stem cells (ESC) indefinitely maintain the pluripotent state of the blastocyst epiblast. Stem cells are invaluable for studying development and lineage commitment, and in livestock they constitute a useful tool for genomic improvement and in vitro breeding programs. Although these cells have been recently derived from bovine blastocysts, a detailed characterization of their molecular state is still lacking. Methods: Here, we compared the transcriptomic and epigenomic profiles of bovine ESC (bESC) obtained from in vitro fertilized (IVF), somatic cell nuclear transfer (SCNT), and parthenogenetic (PAR) embryos. Results: Bovine ESC were efficiently derived from SCNT and IVF embryos and expressed pluripotency markers while retaining genome stability. Transcriptome analysis revealed that only 46 genes were differentially expressed between IVF- and SCNT-derived bESC, which did not reflect significant deviation in cellular function. Additionally, by interrogating the histone marks H3K4me3, H3K9me3 and H3K27me3 with CUT&Tag, we found that the epigenomes of bESC subtypes were virtually indistinguishable. Minor epigenetic differences were randomly distributed throughout the genome and were not associated with differentially expressed or developmentally important genes. Finally, categorization of genomic regions according to their combined histone mark signal demonstrated that bESC subtypes shared the same epigenomic signatures, especially at promoters. Conclusions: Overall, we conclude that bESC derived from SCNT and IVF embryos are transcriptomically and epigenetically analogous.
2022-03-01 | GSE171104 | GEO
Project description:Global hypermethylations of histone H3 lysine 9 (H3K9) tri- and di-methylation (H3K9me3/2) have been identified in bovine cloned embryos at the embryonic genome activation (EGA) stage (eight-cell stage), but the intrinsic reason for these anomalies remains elusive. To ascertain key factors responsible for aberrant H3K9 methylation, we performed RNA sequencing of transcripts in eight-cell bovine in vitro fertilized (IVF) and SCNT embryo. From the differentially expressed genes (DEGs) between IVF and SCNT embryos, we identified that the unsuccessful reactivation of two histone demethylases, KDM4D and KDM4E, is responsible for the incomplete H3K9me3/2 demethylation in SCNT embryos at the EGA stage. By mRNA injection, ectopic expression of either KDM4D or KDM4E could erase H3K9me3/2 barriers, improve blastocyst formation, and elevate cloning efficiency of bovine SCNT. To examine the detailed genes responsive to KDM4E overexpression, we also performed RNA sequencing of bovine eight-cell SCNT embryos with KDM4E compensation and found an obvious restoration of global transcriptional patterns in SCNT embryos. Our study first provides the transcriptome data set of bovine IVF and SCNT embryos during EGA with or without KDM4E overexpression, which advance the understanding of incomplete nuclear reprogramming, and contribute to the practical implications for genetically modified livestock breeding using SCNT.
2018-01-16 | GSE99294 | GEO
Project description:Somatic cell nuclear transfer (SCNT) in mammals has been mostly unsuccessful. In this study, we measured and compared transcription profiles of cloned and fertilized embryos using RNA sequencing. Before zygotic genome activation (ZGA), fewer genes were activated in the cloned embryos than in vitro fertilization (IVF), leading to insufficient activation of protein transport and degradation functions. In blastocysts, terms of “embryo development” and “adherens junction” represented major differences for repressed genes in SCNT compared to IVF. Vitamin C (Vc) was found to relax donor cell chromatin and promote cloned embryo development. RNA sequencing indicated that Vc treatment restored some abnormal genes and processes in the cloned embryos. Processes of autophagy, RNA-editing and cell junction were not fully established, but they were improved by Vc treatment. Overexpression of ZNF641, one of the completely restored genes by Vc treatment, improved the cloned embryos’ potential. Finally, Vc treatment rescued some long non-coding RNAs that were aberrantly expressed in the cloned embryos. Collectively, many important genes and biological processes were abnormal in the cloned embryos, some of which can be improved by Vc treatment. This investigation provides several practical aspects that could be useful for improving cloning efficiency and its future applications.
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Project description:Alternative splicing (AS) is generally observed in different developmental processes in mammals. In mammalian development, totipotency which is defined as the ability of a cell to give rise to all cell types of an entire organism is limited to early-stage preimplantation embryos. Somatic cell nuclear transfer (SCNT) can reprogram terminally differentiated cells into a totipotent state. However, studies addressing the functional role of AS in mammalian preimplantation embryonic development are lacking. Here we show that AS has important physiological functions in mammalian preimplantation embryonic development as a regulator. We discovered abundant AS transitions during both key events in preimplantation embryonic development, fertilization and embryonic genome activation. We also found that the RNA-binding protein hnRNPK govern the oocyte-to-embryo transition by regulating the MII oocyte-specific exon exclusion in mouse. Furthermore, we demonstrated that SCNT embryos had abnormal alternative splicing compared to in vitro fertilized (IVF) embryos in bovine. We used RNA-targeting system CRISPR-Cas13d to target cis elements of ABI2 pre-mRNA to operate alternative splicing, reducing abnormal isoform ratios of SCNT embryos and greatly improve the production of cloned cows. Our results advance the understanding of SCNT-mediated reprogramming and its potential applications for both reproductive and therapeutic cloning.
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2021-06-18 | GSE178436 | GEO
Project description:Somatic cell nuclear transfer (SCNT) into an enucleated oocyte can reprogram a differentiated nucleus to a totipotent state. However, the time course of transcriptional reprogramming has not been determined. To monitor the inactivation of somatic genes after SCNT in the bovine model system, we determined transcript levels of 159 genes highly expressed in fetal fibroblast nuclear donor cells, but not in metaphase II recipient oocytes. For 18 of these genes significantly higher transcript levels were found in four-cell SCNT embryos compared with four-cell embryos derived by in vitro fertilization (IVF), indicating incomplete silencing of somatic genes at this stage. RNA sequencing revealed that nearly 600 genes with no transcripts in oocytes were activated in eight-cell IVF embryos, in agreement with major embryonic genome activation (EGA). De novo transcription in SCNT embryos was delayed (16 genes before the 16-cell stage, 300 and >800 genes at the 16-cell and blastocyst stages). Intron-containing primary transcripts as another option to detect embryonic gene transcription revealed activation of >2,200 genes in IVF embryos at the eight-cell stage, while only 828 genes were activated in SCNT embryos. At the 16-cell stage, a higher number of activated genes was found in SCNT (1,917) than in IVF embryos (738). Self-organizing tree algorithm clustering confirmed that in SCNT embryos transcription of genes that are normally activated during major EGA is delayed. Our study provides detailed insight into the timing of genome activation in cloned embryos that is substantially different from IVF embryos in spite of similar developmental kinetics.
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Project description:Porcine parthenogenetic embryos along with biparental control embryos were used to investigate imprinted genes in chromosome 11.
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