Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin architecture reorganization in somatic cell nuclear transfer embryos

ABSTRACT: The oocyte cytoplasm can reprogram somatic cell nucleus into a totipotent state but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examined higher-order chromatin structures of mouse SCNT embryos using an optimized low-input Hi-C approach. We found that the donor cell chromatin transformed to metaphase state rapidly after injection along with the dissolution of typical 3D chromatin structures. Intriguingly, the donor cell genome underwent a transition from mitotic metaphase-like state to meiosis metaphase II-like state within one hour after activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerged at 6 hours after activation. Then TADs were gradually removed until the 2-cell stage and then progressively reestablished. We found that relative few distal (> 2 Mb) interactions were present in 2-cell stage SCNT embryos. Also, obvious differences in compartment and TAD organization between fertilization-derived and SCNT embryos were observed in early stages (2-8 cell stages). Many interactions between super-enhancers and promoters were not successfully established in SCNT embryos, and these interactions were further shown important for zygotic genome activation (ZGA). Moreover, we demonstrate that the aberrant chromatin architecture reorganization in SCNT embryos may be due to the persistent H3K9me3 and can be partially rescued by the Kdm4d overexpression. This study therefore provides novel insight into chromatin architecture reorganization during SCNT embryo development.

ORGANISM(S): Mus musculus

PROVIDER: GSE146001 | GEO | 2020/02/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Analysis of genome architecture during SCNT reveals a role of cohesin in impeding minor ZGA

Project description:Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of three-dimensional chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger TADs at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.

2020-06-23 | GSE139430 | GEO

Histone variant H3.3 is an essential maternal factor for oocyte reprogramming

Project description:Mature oocyte cytoplasm can reprogram somatic cell nuclei to the pluripotent state through a series of sequential events including protein exchange between the donor nucleus and ooplasm, chromatin remodeling, and pluripotency gene reactivation. Maternal factors that are responsible for this reprogramming process remain largely unidentified. Here, we demonstrate that knockdown of histone variant H3.3 in mouse oocytes results in compromised reprogramming and down-regulation of key pluripotency genes; and this compromised reprogramming both for developmental potentials and transcription of pluripotency genes can be rescued by injecting exogenous H3.3 mRNA, but not H3.2 mRNA into oocytes in somatic cell nuclear transfer (SCNT) embryos. We show that maternal H3.3, and not H3.3 in the donor nucleus, is essential for successful reprogramming of somatic cell nucleus into the pluripotent state. Furthermore, H3.3 is involved in this reprogramming process by remodeling the donor nuclear chromatin through replacement of donor nucleus-derived H3 with de novo synthesized maternal H3.3 protein. Our study shows that H3.3 is a crucial maternal factor for oocyte reprogramming and provides a practical model to directly dissect the oocyte for its reprogramming capacity. Transcriptome sequencing of 4-cell NT embryos, Luciferase 4-cell SCNT embryos, 4-cell NT embryos_H3.3KD, 4-cell NT embryos_H3.3KD+H3.3mRNA, H3.3 KD + H3.2 mRNA SCNT embryos

2014-06-02 | E-GEOD-56762 | biostudies-arrayexpress

RNA-Seq analysis of in vitro cultivated bovine fetal fibroblasts (BFF116)

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 | GSE125828 | GEO

Time course of transcriptional reprogramming in bovine nuclear transfer embryos

2021-05-31 | GSE125724 | GEO

Reprogramming of chromatin accessibility in somatic cell nuclear transfer is DNA replication independent

Project description:Mammalian oocytes have the ability to reset the transcriptional program of differentiated somatic cells into that of totipotent embryos through somatic cell nuclear transfer (SCNT). However, the mechanisms underlying SCNT-mediated reprogramming are largely unknown. To understand the mechanisms governing chromatin reprogramming during SCNT, we profiled DNaseI hypersensitive sites (DHSs) in donor cumulus cells and 1-cell stage SCNT embryos. To our surprise, the chromatin accessibility landscape of the donor cells is drastically changed to recapitulate that of the in vitro fertilization (IVF)-derived zygotes within 12 hours. Interestingly, this DHS reprogramming takes place even in the presence of a DNA replication inhibitor, suggesting that SCNT-mediated DHS reprogramming is independent of DNA replication. Thus, the study not only reveals the rapid and drastic nature of the changes in chromatin accessibility through SCNT, but also provides a DNA replication-independent model for studying cellular reprogramming.

2018-05-14 | GSE110851 | GEO

Identification of epigenetic barrier that prevents reprogramming in somatic cell nuclear transfer

Project description:Mammalian oocytes can reprogram somatic cells into totipotent state, which allows animal cloning through somatic cell nuclear transfer (SCNT). However, the great majority of SCNT embryos fail to develop to term due to poorly defined reprogramming defects. Here we demonstrate that histone H3 lysine 9 trimethylation (H3K9me3) in donor nuclei is a major epigenetic barrier that prevents efficient nuclear reprogramming in mouse oocytes. Comparative transcriptome analysis of early embryos revealed reprogramming resistant regions (RRRs) where transcriptional activation at 2-cell embryos is inhibited by SCNT compared to in vitro fertilization (IVF). RRRs significantly overlap with H3K9me3 enrichment in donor somatic cells. Importantly, removal of the H3K9me3 by ectopic expression of an H3K9me3 demethylase Kdm4d in recipient oocytes not only reactivates most RRRs, but also greatly improves development of SCNT embryos. Furthermore, the use of Suv39h1/2-depleted somatic nuclei as donors also greatly improves the development of SCNT embryos. Our study thus reveals H3K9me3 as an epigenetic barrier in SCNT-mediated reprogramming and provides a feasible method for improving mammalian cloning efficiency.

2014-11-07 | GSE59073 | GEO

SCNT embryos are defective for H3K27me3 imprinting [RNA-seq]

Project description:Animal cloning can be achieved through somatic cell nuclear transfer (SCNT), yet the success rate remains very low. Recent studies have revealed two epigenetic barriers, H3K9me3 in donor cells and abnormal Xist activation, that impede SCNT reprogramming. Here we overcome both barriers by combining the use of Xist knockout donor cells and overexpressing Kdm4d, which allowed us to achieve the highest mouse cloning efficiency. However, SCNT-associated developmental defects and abnormal placenta were still observed, suggesting the existence of additional epigenetic defects in these SCNT embryos. Comparative DNA methylome analysis of IVF and SCNT blastocysts identified many abnormally methylated regions in SCNT embryos, despite successful global methylome reprogramming. Strikingly, allelic transcriptome analyses of SCNT blastocysts revealed a complete loss-of-imprinting at the H3K27me3-dependent imprinted genes, which may account for postimplantation developmental defects of SCNT embryos. This study thus not only provides the most efficient method for mouse cloning but also points the way for further improve SCNT cloning.

2018-06-27 | GSE109214 | GEO

SCNT embryos are defective for H3K27me3 imprinting [Bisulfite-seq]

2018-06-27 | GSE112528 | GEO

SCNT embryos are defective for H3K27me3 imprinting [ChIP-seq]

Project description:Animal cloning can be achieved through somatic cell nuclear transfer (SCNT), yet the success rate is very low. Recent studies have revealed H3K9me3 in donor cells and abnormal Xist activation as epigenetic barriers that impede SCNT reprogramming. Here we overcome both barriers by using Xist knockout donor cells combined with overexpressing Kdm4d and achieved the highest cloning efficiency in mice. However, post-implantation developmental defects and abnormal placenta were still observed, indicating presence of additional epigenetic barriers impedes SCNT cloning. Comparative DNA methylome analysis of IVF and SCNT blastocysts identified many abnormally methylated regions in SCNT embryos, despite successful global methylome reprogramming. Strikingly, allelic transcriptome and ChIP-seq analyses of preimplantation SCNT embryos revealed a complete loss of H3K27me3 imprinting, which likely accounts for postimplantation developmental defects of SCNT embryos. This study not only provides an efficient method for mouse cloning, but also paves the way for further improving SCNT cloning efficiency.

2018-06-27 | GSE114307 | GEO

Histone Demethylase-Assisted Somatic Cell Nuclear Transfer Facilitates Derivation of Human Pluripotent Stem Cells

Project description:The extremely low efficiency of human embryonic stem cell (hESC) derivation using somatic cell nuclear transfer (SCNT) limits potential application. Blastocyst formation from human SCNT embryos occurs at a low rate and with only some oocyte donors. We previously showed in mice that reduction of histone H3 lysine 9 trimethylation (H3K9me3) through ectopic expression of the H3K9me3 demethylase Kdm4d greatly improves SCNT embryo development. Here we show that overexpression of a related H3K9me3 demethylase KDM4A improves human SCNT, and that, as in mice, H3K9me3 in the human somatic cell genome is an SCNT reprogramming barrier. Overexpression of KDM4A significantly improves the blastocyst formation rate in human SCNT embryos by facilitating transcriptional reprogramming, allowing derivation of NTESCs from all oocyte donors tested using adult AMD patient somatic nuclei donors. This conserved mechanistic insight has potential applications for improving SCNT in a variety of contexts, including regenerative medicine. Here we perform RNA-seq based transcriptome profiling in human Donor (fibroblast cells), in vitro fertilized embryos at 8-cell stages (IVF_8Cell), somatic cell nuclear transfer embryos at 8-cell stages (SCNT_8Cell), SCNT assisted by KDM4A 8-cell embryos (SCNT_KDM4A_8Cell). Besides, we also perform RNA-seq in Control human ES cells (CTR_hES) and SCNT assisted by KDM4A derived human ES cells (NTK) with duplicates.Â

2016-03-01 | E-GEOD-73362 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data