KDM6A improves the efficiency of nuclear transfer reprogramming in bovine
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA471880 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7179550_1.fastq.gz | Fastqsanger.gz | |||
| SRR7179550_2.fastq.gz | Fastqsanger.gz | |||
| SRR7179551_1.fastq.gz | Fastqsanger.gz | |||
| SRR7179551_2.fastq.gz | Fastqsanger.gz | |||
| SRR7179552_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
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: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
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: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.
2016-03-01 | GSE73362 | GEO
Project description:Aberrant epigenetic reprogramming is one of the major barriers for somatic cell reprogramming. Although our previous study has demonstrated that KDM6A, a H3K27me3 demethylase, could improve nuclear reprogramming efficiency, but its role in somatic cell reprogramming and the mechanism remain unclear. In this study, we demonstrated that overexpression of Kdm6a could improve iPSC reprogramming efficiency in a demethylase enzymatic activity-dependent manner. And Kdm6a overexpression changed the gene expression profile and metabolic pattern through erasing the repressive H3K27me3 in fibroblast. Besides, we proved that KDM6A could promote IL-6 expression in MEF cells and the secreted IL-6 also could improve iPSC reprogramming efficiency. Furthermore, we found that KDM6A could promote PTEN expression, further regulate p-AKT and p-mTOR levels, which favor the reprogramming, and interference of PTEN could counteracted the promotion effect of KDM6A. Taken together, our data revealed that KDM6A could promote iPSC reprogramming efficiency by accelerate the change of gene expression profile and metabolic pattern in a demethylation-activity-dependent manner, which may give insight to the relationship between epigenetic modification and somatic cell reprogramming.
2021-10-20 | GSE138816 | GEO
Project description:Aberrant epigenetic reprogramming is one of the major barriers for somatic cell reprogramming. Although our previous study has demonstrated that KDM6A, a H3K27me3 demethylase, could improve nuclear reprogramming efficiency, but its role in somatic cell reprogramming and the mechanism remain unclear. In this study, we demonstrated that overexpression of Kdm6a could improve iPSC reprogramming efficiency in a demethylase enzymatic activity-dependent manner. And Kdm6a overexpression changed the gene expression profile and metabolic pattern through erasing the repressive H3K27me3 in fibroblast. Besides, we proved that KDM6A could promote IL-6 expression in MEF cells and the secreted IL-6 also could improve iPSC reprogramming efficiency. Furthermore, we found that KDM6A could promote PTEN expression, further regulate p-AKT and p-mTOR levels, which favor the reprogramming, and interference of PTEN could counteracted the promotion effect of KDM6A. Taken together, our data revealed that KDM6A could promote iPSC reprogramming efficiency by accelerate the change of gene expression profile and metabolic pattern in a demethylation-activity-dependent manner, which may give insight to the relationship between epigenetic modification and somatic cell reprogramming.
2021-10-20 | GSE138815 | GEO
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
Project description:Derivation of embryonic stem cells (ESC) genetically identical to a patient by somatic cell nuclear transfer (SCNT) holds the potential to cure or alleviate the symptoms of many degenerative diseases while circumventing any immunorejection issues. However, no primate nuclear transfer embryonic stem (ntES) cell lines have been derived to date. Here, we used a modified SCNT technique to produce rhesus macaque SCNT blastocysts at a relatively high efficiency from adult donor cells and we successfully derived two primate ntES cell lines from 304 oocytes (an overall efficiency of 0.7%). Nuclear and mitochondrial DNA analysis confirmed the ntES cell lines were derived from rhesus monkey SCNT blastocysts and both rhesus monkey ntES cell lines exhibited a normal ESC morphology, expressed key stemness markers, were transcriptionally indistinguishable from control ESC lines and differentiated into multiple cell types. This is, to our knowledge, the first confirmed derivation of primate ntES cell lines. Keywords: rhesus monkey somatic cell nuclear transfer embryonic stem cells
2007-08-29 | GSE7748 | 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.
2017-04-15 | GSE95053 | GEO
Project description:Since the first cloned animal Dolly Sheep was successfully created by using somatic cell nuclear transfer(SCNT) technique. It has become an irreplaceable tool to understand nuclear reprogramming and totipotency and holds huge potentials for regenerative medicine. However, extremely poor development rate of SCNT embryos indicates it is still questionable. The nature of reprogramming oocyte factors and their mechanism of action remain largely unknown.It is evident that the major barrier that hinders the developing iSCNT embryo mainly appears at the time of embryonic genome activation (EGA), which primarily occurs at the eight-cell stage in mammalian. The interspecies somatic cell nuclear transfer (iSCNT) is desired model for nuclear reprogramming research and a powerful tool for discovering the master genome activation genes. In this study, a valuable transcriptome recourse of iSCNT embryos was established, which derived from more than 2000 clone embryos of four different inter-family donor cells. Based on weighted gene co-expression network (WGCNA) approach, we provide an extensive transcriptome analysis of differentially expressed genes(DEG) for iSCNT embryos. The total gene expression patterns of different iSCNT embryos were discussed. 26 cell-specific modules with were identified, and those module significance and GO enriched categories were analyzed. The regulatory pathways of reprogramming barriers were further enriched. As master genome trigger genes, the transcripts related to TFIID subunit, RNA polymerase and Mediator were incomplete activated in iSCNT embryos. This indicated that pioneer factors, present in the cytoplasm of the oocyte, were failed to bind the sequence target on the heterology nuclear genome. This genomic incompatibility between the nuclear donor cell and the cytoplast may be as a major contributing factor causes the developmental failure of iSCNT cloned embryos. This study demonstrates that the iSCNT embryos undergoes only partial or incomplete reprogramming at eight-cell stage in mammalian. Our results offered convincing evidence that the abnormal expression of key master pathways may be caused the embryo developmental block of cloning embryo. This work will contribute to a better understanding of the molecular interaction between nuclear–cytoplasmic interaction and provides insight into the molecular determinants of nuclear reprogramming, human embryonic stem cell (hESC)-based therapies and rescuing highly endangered species.
2016-11-01 | GSE89279 | GEO