Time course of transcriptional reprogramming in bovine nuclear transfer embryos
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA517402 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8494650.fastq.gz | Fastqsanger.gz | |||
| SRR8494651.fastq.gz | Fastqsanger.gz | |||
| SRR8494652.fastq.gz | Fastqsanger.gz | |||
| SRR8494653.fastq.gz | Fastqsanger.gz | |||
| SRR8494654.fastq.gz | Fastqsanger.gz |
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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.
2021-05-31 | GSE125724 | GEO
Project description:Although somatic cell nuclear transfer (SCNT) cloning is more efficient in bovine than in all other species tested so far, there is a high rate of pregnancy failure that has been linked to structural and functional abnormalities of the placenta. We tested the hypothesis that these changes may originate from disturbed embryo-maternal interactions in the pre-implantation period. Therefore, we evaluated the transcriptome response of the endometrium to SCNT embryos (produced from five different donor cell cultures) as compared to embryos derived from in vitro fertilization (IVF). SCNT embryos and IVF embryos were cultured under identical conditions to the blastocyst stage (Day 8) and transferred to recipients. The recipients were slaughtered at day 18 of pregnancy and the uterus was recovered. Pregnancy was verified by the presence of at least one normally developed embryo. Transcriptome profiling of endometrium samples using a custom cDNA microarray covering transcripts expressed in the endometrium and/or oviduct epithelium revealed 58 transcripts that were differently abundant between endometrium samples from SCNT vs. IVF pregnancies. Prominent examples are NR2F2 (encoding the orphan nuclear receptor COUP-TFII) and GJA1 (encoding connexin 43). Both transcripts are known to play important roles in placentation and were significantly less abundant in endometrium from SCNT vs. IVF pregnancies. These findings suggest that placental failure in bovine clone pregnancies may originate from abnormal embryo-maternal communication already in the pre- or peri-implantation period. Endometrium transcriptome profiles may serve as a novel readout to evaluate SCNT embryos for their ability to induce pregnancy with a functional placenta. Keywords: response to different embryos Nineteen German Fleckvieh (Simmental) heifers were slaughtered at day 18 of pregnancy. Cycle-synchronized recipient heifers received either IVP or SCNT embryos at day 7 of the estrous cycle. Animals were slaughtered at day 18. Endometrial (intercaruncular) tissue samples were obtained from 10 pregnant animals after transfer of IVP embryos and from 9 pregnant animals after transfer of SCNT embryos.
2009-03-12 | E-GEOD-13663 | biostudies-arrayexpress
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236608 | GEO
Project description:Although somatic cell nuclear transfer (SCNT) cloning is more efficient in bovine than in all other species tested so far, there is a high rate of pregnancy failure that has been linked to structural and functional abnormalities of the placenta. We tested the hypothesis that these changes may originate from disturbed embryo-maternal interactions in the pre-implantation period. Therefore, we evaluated the transcriptome response of the endometrium to SCNT embryos (produced from five different donor cell cultures) as compared to embryos derived from in vitro fertilization (IVF). SCNT embryos and IVF embryos were cultured under identical conditions to the blastocyst stage (Day 8) and transferred to recipients. The recipients were slaughtered at day 18 of pregnancy and the uterus was recovered. Pregnancy was verified by the presence of at least one normally developed embryo. Transcriptome profiling of endometrium samples using a custom cDNA microarray covering transcripts expressed in the endometrium and/or oviduct epithelium revealed 58 transcripts that were differently abundant between endometrium samples from SCNT vs. IVF pregnancies. Prominent examples are NR2F2 (encoding the orphan nuclear receptor COUP-TFII) and GJA1 (encoding connexin 43). Both transcripts are known to play important roles in placentation and were significantly less abundant in endometrium from SCNT vs. IVF pregnancies. These findings suggest that placental failure in bovine clone pregnancies may originate from abnormal embryo-maternal communication already in the pre- or peri-implantation period. Endometrium transcriptome profiles may serve as a novel readout to evaluate SCNT embryos for their ability to induce pregnancy with a functional placenta. Keywords: response to different embryos
2009-03-13 | GSE13663 | GEO
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236604 | GEO
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236605 | GEO
Project description:Individual zona free in vitro grown bovine day 7 blastocysts were compared to stage and quality matched nuclear transfer derived blastocysts (fibroblast donor cells).
2006-02-14 | E-MEXP-556 | biostudies-arrayexpress
Project description:As a histone hallmark for transcription repression, Histone H3 lysine 27 trimethylation (H3K27me3) plays important roles in mammalian embryo development and induced pluripotent stem cells (iPSCs) generation. However, the expression profile and roles of H3K27me3 in bovine somatic cell nuclear transfer (SCNT) reprogramming remain poorly understood. In this study, we find SCNT embryos exhibit global hypermethylation of H3K27me3 from two-cell to eight-cell stage and its removal by ectopically expressed H3K27me3 demethylase-KDM6A could greatly improves SCNT efficiency. To illuminate the mechanism of improving SCNT reprogramming efficiency of KDM6A overexpression, we performed RNA sequencing of transcripts in SCNT morula with or without KDM6A overexpression. RNA-seq reveal that KDM6A overexpression could enhance transcription of genes mainly involved cell adhesion and cellular metabolism process, as well as X-linked genes. We first provides the transcriptome data of bovine SCNT morula with or without KDM6A overexpression. Meanwhile, we compared the differences of transcriptome between SCNT eight-cell embryos and morula. Our study provide a more promising approach to improving the efficiency of SCNT reprogramming and contribute to understanding the mechanism of first cell fate determine during embryo development in bovine.
2019-01-31 | GSE114596 | GEO
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236607 | GEO
Project description:Animal cloning has been achieved in many species by transplanting differentiated cell nuclei to unfertilized oocytes. However, the low efficiencies of cloning have remained an unresolved issue. We find that the combination of two small molecules, trichostatin A (TSA) and vitamin C (VC), under culture condition with deionized bovine serum albumin (dBSA), dramatically improves the cloning efficiency in mice and 15% of cloned embryos develop to term by means of somatic cell nuclear transfer (SCNT). RNA-seq analyses of SCNT embryos at the 2-cell stage revealed that the treatment with TSA, followed by the VC treatment, resulted in the upregulated expression of the previously identified reprogramming-resistant genes. Moreover, the expression of 2-cell-specific retroelements was upregulated by the sequential treatment with TSA and VC. The best condition for reprogramming is to add TSA for 8 hours after nuclear transfer and then SCNT embryos are further cultured with VC for 7 hours.
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