Gene resistance to transcriptional reprogramming following nuclear transfer is directly mediated by multiple chromatin repressive pathways
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA347982 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4417750.fastq.gz | Fastqsanger.gz | |||
| SRR4417760.fastq.gz | Fastqsanger.gz | |||
| SRR4417770.fastq.gz | Fastqsanger.gz | |||
| SRR4417780.fastq.gz | Fastqsanger.gz | |||
| SRR4417790.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:Understanding the mechanism of resistance of certain genes to reactivation will help improving the success of nuclear reprogramming. Here, in a Xenopus oocyte nuclear transfer assay we identify mouse genes that are resistant to reprogramming by oocyte factors. By using MEF nuclei with WT or reduced DNA methylation in combination with chromatin modifiers able to erase H3K9me3, H3K27me3, and H2Aub from transplanted nuclei, we reveal the basis for resistance to transcriptional reprogramming. We observe a complex relationship between loss of resistance and chromatin modifiers treatment as a majority of gene is affected by more than one type of treatment, suggesting that resistance requires simultaneous repression through multiple epigenetic mechanisms. Existence of synergistic as well as adverse mechanism of action of chromatin modifiers on removal of resistance is revealed by the classification of resistant genes according to their sensitivity to chromatin modifiers treatments. We further demonstrate that removal of H2Aub from transplanted chromatin explain loss of resistance upon USP21 expression. Finally, we provide evidence that H2A ubiquitylation is also contributing to resistance to transcriptional reprogramming in mouse nuclear transfer embryos.
2017-06-12 | GSE87872 | GEO
Project description:Understanding the mechanism of resistance of genes to reactivation will help improve the success of nuclear reprogramming. Using mouse embryonic fibroblast nuclei with normal or reduced DNA methylation in combination with chromatin modifiers able to erase H3K9me3, H3K27me3, and H2AK119ub1 from transplanted nuclei, we reveal the basis for resistance of genes to transcriptional reprogramming by oocyte factors. A majority of genes is affected by more than one type of treatment, suggesting that resistance can require repression through multiple epigenetic mechanisms. We classify resistant genes according to their sensitivity to 11 chromatin modifier combinations, revealing the existence of synergistic as well as adverse effects of chromatin modifiers on removal of resistance. We further demonstrate that the chromatin modifier USP21 reduces resistance through its H2AK119 deubiquitylation activity. Finally, we provide evidence that H2A ubiquitylation also contributes to resistance to transcriptional reprogramming in mouse nuclear transfer embryos.
| S-EPMC5344684 | biostudies-literature
Project description:Reprogramming occurs after nuclear transfer into zygotes whose genome was removed in mitosis, but not after nuclear transfer into zygotes enucleated in interphase Egli et al. Development 2010 doi:10.1242/dev.046151 Groups of 20 mouse embryos were used for the analysis. RNA amplification was done using Illumina total prep RNA amplification kit. Total of 21 arrays.
2010-05-27 | E-GEOD-21609 | biostudies-arrayexpress
Project description:Reprogramming occurs after nuclear transfer into zygotes whose genome was removed in mitosis, but not after nuclear transfer into zygotes enucleated in interphase Egli et al. Development 2010 doi:10.1242/dev.046151
2010-05-01 | GSE21609 | GEO
Project description:Production of viable and fertile mice have been reported by nuclear replacement, however, the reasons behind the frequent deformations among foetuses and progeny are not well understood. Activation and in vitro culture methods are also important. Origin of the nuclear donor cells affects success rates, and their survival in culture varies. It has been reported that offspring of nuclear replacement parental mice were normal and fertile. All epigenetic problems in the parents seem to be erased when cell nuclei go through the germ line. cDNA microarray analysis compared expression patterns of Dll1 ko versus Dll1 ko NT (NT = nuclear transfer) and wt versus wt NT of liver and spleen. The aim of this study was analysis of possible epigenetic effects by cloning in the offspring of the 3rd generation. If the 3rd generation cloned animals are indeed phenotypically equivalent to conventional transgenic mouse models then this would open the possibility to develop novel techniques of genetic engineering based on somatic gene targeting and nuclear replacement. four male animals of each cohort (Dll1 conventional transgenic mouse, Dll1 nuclear transfer mouse, wildtype, wildtye nuclear transfer mouse). Two technical replicates including a colour flip experiment. For each analysed organ (liver, spleen) eight experiments including four biological replicates. As reference RNA pools were used
2011-01-01 | E-GEOD-20560 | biostudies-arrayexpress
Project description:Reprogramming occurs after nuclear transfer into zygotes whose genomes have been removed in mitosis, but not after nuclear transfer into zygotes enucleated in interphase. Our results suggest that there is a previously unappreciated barrier to successful human nuclear transfer, and that future studies should focus on the requirements for somatic genome activation.
2011-10-04 | GSE24631 | GEO
Project description:Reprogramming occurs after nuclear transfer into zygotes whose genomes have been removed in mitosis, but not after nuclear transfer into zygotes enucleated in interphase. Our results suggest that there is a previously unappreciated barrier to successful human nuclear transfer, and that future studies should focus on the requirements for somatic genome activation. 1-3 embryos were used for analysis. RNA amplification was done using two or three rounds of T7-mediated RNA amplification using the Illumina Total Prep RNA Amplification kit. Somatic cells 1-000 and 1-011 required only one round of RNA amplification because starting amounts of RNA were 100-500ng, while embryonic samples were amplified from single cells or embryos.
2011-10-03 | E-GEOD-24631 | biostudies-arrayexpress
Project description:Whereas cloning mammals by direct somatic cell nuclear transfer has been successful using a wide range of donor cell types, neurons from adult brain remain M-bM-^@M-^\unclonableM-bM-^@M-^] for unknown reasons. Here we examined whether neurons from adult mice could be cloned, using a combination of two epigenetic approaches. First, we used a specific antibody to discover cell types with reduced amounts of a repressive histone mark - dimethylated histone H3 lysine 9 (H3K9me2) - and identified CA1 pyramidal cells in the hippocampus and Purkinje cells in the cerebellum as candidates. Second, reconstructed embryos were treated with trichostatin A (TSA), a potent histone deacetylase inhibitor. Using CA1 cells, cloned offspring were obtained at high rates, reaching 10.2% and 4.6% (per embryos transferred) for male and female donors, respectively. Cerebellar Purkinje cell nuclei were too large to maintain their genetic integrity during nuclear transfer, leading to developmental arrest of embryos. However, gene expression analysis using cloned blastocysts corroborated a high rate of genomic reprogrammability of CA1 pyramidal and Purkinje cells. Neurons from the hippocampal dentate gyrus and cerebral cortex, which had higher amounts of H3K9me2, could also be used for producing cloned offspring, but the efficiencies were low. A more thorough analysis revealed that TSA treatment was essential for cloning adult neuronal cells. This study demonstrated for the first time that adult neurons could be cloned by nuclear transfer. Furthermore, our data imply that reduced amounts of H3K9me2 and increased histone acetylation appear to act synergistically to improve the development of cloned embryos. Comparative gene expression analyses using blastocysts of cloned embryos were performed by microarray. Cloned embryos were produced with three different types of donor cells (neonatal Sertoli cells, CA1 pyramidal cells and Purkinje cells) and all cloned embryos were treated with Trichostatin A (TSA). Each embryos were cultured for 96 h and blastocysts derived from each donor cell types were subjected to gene expression microarray. For comparison of gene expression, the data sets of control sex- and genotype-matched embryos produced by in vitro fertilization and SCNT-derived blastocysts from cumulus cells treated with TSA from our previous paper (Inoue K. et al. Science 2010) were also used.
2015-02-03 | E-GEOD-65497 | 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:Whereas cloning mammals by direct somatic cell nuclear transfer has been successful using a wide range of donor cell types, neurons from adult brain remain “unclonable” for unknown reasons. Here we examined whether neurons from adult mice could be cloned, using a combination of two epigenetic approaches. First, we used a specific antibody to discover cell types with reduced amounts of a repressive histone mark - dimethylated histone H3 lysine 9 (H3K9me2) - and identified CA1 pyramidal cells in the hippocampus and Purkinje cells in the cerebellum as candidates. Second, reconstructed embryos were treated with trichostatin A (TSA), a potent histone deacetylase inhibitor. Using CA1 cells, cloned offspring were obtained at high rates, reaching 10.2% and 4.6% (per embryos transferred) for male and female donors, respectively. Cerebellar Purkinje cell nuclei were too large to maintain their genetic integrity during nuclear transfer, leading to developmental arrest of embryos. However, gene expression analysis using cloned blastocysts corroborated a high rate of genomic reprogrammability of CA1 pyramidal and Purkinje cells. Neurons from the hippocampal dentate gyrus and cerebral cortex, which had higher amounts of H3K9me2, could also be used for producing cloned offspring, but the efficiencies were low. A more thorough analysis revealed that TSA treatment was essential for cloning adult neuronal cells. This study demonstrated for the first time that adult neurons could be cloned by nuclear transfer. Furthermore, our data imply that reduced amounts of H3K9me2 and increased histone acetylation appear to act synergistically to improve the development of cloned embryos.
2015-02-03 | GSE65497 | GEO