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Chromatin architecture reorganization in somatic cell nuclear transfer embryos

ABSTRACT: Chromatin architecture reorganization in somatic cell nuclear transfer embryos

PROVIDER: PRJNA608976 | ENA |

REPOSITORIES: ENA

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Chromatin architecture reorganization in somatic cell nuclear transfer embryos

Project description: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.

2020-02-27 | GSE146001 | GEO

Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos.

Project description: Not available

| S-EPMC7156422 | biostudies-literature

Genome-wide comparison of EpiSC lines derived from fertilized (FT) and somatic cell nuclear transfer (NT) embryos

Project description:Genome wide comparison of gene expression between EpiSC lines derived from fertilized (FT) embryos and somatic cell nuclear transfer (NT) embryos. EpiSC lines were derived from fertilized and somatic cell nuclear transfer embryos and cultured until 15 to 20 passages. RNA was then extracted in order to compare transcriptomic profiles.

2010-02-05 | GSE17402 | GEO

Dynamic reorganization of nuclear architecture during human cardiogenesis

Project description:Dynamic reorganization of nuclear architecture during human cardiogenesis

| PRJNA417681 | ENA

Transcriptional reprogramming of somatic cells after nuclear transfer to mouse 4-cell embryos

Project description:We have developed a nuclear transfer (NT) system in which somatic nuclei are transplanted into mouse embryos arrested at the 4-cell stage. The transplanted somatic nuclei show swelling and epigenetic reprogramming towards 4-cell-like nuclei. To assess genome-wide transcriptional reprogramming of the injected nuclei, the newly transcribed genes in NT embryos were examined by RNA-seq analyses. As a control, NT was also performed using mouse embryos at the 2-cell stage.

2021-11-03 | GSE162345 | GEO

Suppression of endogenous retroviral enhancers in somatic cell nuclear transfer embryos

Project description:Endogenous retroviruses (ERVs) in the mammalian genome play diverse roles in embryonic development. These development-related ERVs are generally repressed in somatic cells and are therefore likely repressed in embryos derived from somatic cell nuclear transfer (SCNT). In this study, we sought to identify ERVs that are repressed in SCNT-derived morula embryos, which may consequently cause previously unexplained embryonic deaths shortly after implantation. Our transcriptome analysis revealed that, amongst ERV families, ERVK was specifically and strongly downregulated in SCNT embryos while other transposable elements including LINE and ERVL were unchanged. Among subfamilies of ERVK, RLTR45-int was most repressed in SCNT embryos despite its highest expression in control fertilized embryos. Interestingly, the nearby genes (within 5–50 kb, n = 19) of the repressed RLTR45-int loci were also repressed in SCNT embryos with a significant correlation between them. Furthermore, lysine H3K27 acetylation was enriched around the RLTR45-int loci. These findings indicate that RLTR45-int elements function as enhancers of nearby genes. Indeed, deletion of two sequential RLTR45-int loci on chromosome 4 or 18 resulted in downregulations of nearby genes at the morula stage. We also found that RLTR45-int loci, especially SCNT-low, enhancer-like loci, were strongly enriched with H3K9me3, a repressive histone mark. Importantly, these H3K9me3-enriched regions were resistant to histone demethylase Kdm4d in SCNT embryos. Thus, we identified ERVK subfamily RLTR45-int, putative enhancer elements, as a strong reprogramming barrier for SCNT. A large-scale downregulations of their regulating genes in SCNT morulae might cumulatively affect postimplantation development of SCNT embryos.

2022-10-08 | GSE214878 | GEO

Dynamic reorganization of nuclear architecture during human cardiogenesis [RNA-seq]

Project description:Dynamic reorganization of nuclear architecture during human cardiogenesis [RNA-seq]

| PRJNA417683 | ENA

Dynamic reorganization of nuclear architecture during human cardiogenesis [ATAC-seq]

Project description:Dynamic reorganization of nuclear architecture during human cardiogenesis [ATAC-seq]

| PRJNA417684 | ENA

Dynamic reorganization of nuclear architecture during human cardiogenesis [HiC-seq]

Project description:Dynamic reorganization of nuclear architecture during human cardiogenesis [HiC-seq]

| PRJNA417685 | ENA

Expression data from somatic cell nuclear transfer bovine embryo

Project description:Expression data from somatic cell nuclear transfer bovine embryo