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Novel culture systems for naive human embryonic stem cells based on chemical molecule screening [RNA-seq]

ABSTRACT: We systematically screened novel culture systems designed for naïve human embryonic stem cells via high-content screening and small molecule combinations. Our findings indicate that the cell lines established through this innovative system closely mimic the in vivo Inner Cell Mass (ICM) concerning both transcriptome profiles and methylation patterns. Additionally, we observed an elevated level of methylation specifically on transposable elements within these cell lines. Furthermore, our investigations suggest that the genomic stability of this novel system may exhibit superior qualities.

ORGANISM(S): Homo sapiens

PROVIDER: GSE252312 | GEO | 2025/12/01

REPOSITORIES: GEO

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Novel culture systems for naive human embryonic stem cells based on chemical molecule screening [WGBS]

Project description:We systematically screened novel culture systems designed for naïve human embryonic stem cells via high-content screening and small molecule combinations. Our findings indicate that the cell lines established through this innovative system closely mimic the in vivo Inner Cell Mass (ICM) concerning both transcriptome profiles and methylation patterns. Additionally, we observed an elevated level of methylation specifically on transposable elements within these cell lines. Furthermore, our investigations suggest that the genomic stability of this novel system may exhibit superior qualities.

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Novel culture systems for naive human embryonic stem cells based on chemical molecule screening

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-12-01 | GSE252316 | GEO

Distinct distribution of H3K27me3 and DNA methylation stabilizes the segregation of extraembryonic and embryonic lineages

Project description:One of the most important topic in mammalian embryogenesis is cell lineage segregation. Briefly, one totipotent zygote will develop into inner cell mass (ICM) and trophectoderm (TE) at blastocyst stage, then the ICM will finally develop into multiple somatic cell lineages and TE will majorly become the placenta tissue which supports and protects the development of the embryo proper. Multiple extrinsic and intrinsic regulatory pathways are involved in facilitating the appropriate development of the embryo. Epigenetic reprogramming is one of the most pervasive events during mouse embryo development(Li, 2002). Recent studies had implied that distinct features for the establishment of DNA methylation(Monk et al., 1987) and histone modifications especially H3K27me3(Liu et al., 2016) during mouse early embryo development. The re-establishment of DNA methylation in early mouse embryos starts at blastocyst stage (about embryonic day 3.5, E3.5) and peaks around the gastrulation stage, while the re-establishment of H3K27me3 exhibits a great level of dynamics and gradually increased CpG preference during pre-implantation embryo development(Liu et al., 2016). However, the underlying epigenetic mechanism concerning the lineage segregation and developmental competence restriction between the pluripotent embryo proper and the supporting extraembryonic tissues especially extraembryonic ectoderm (ExE) remains largely unknown. Surprisingly, no significant difference exists for the distribution of H3K27me3 and DNA methylation between ICM and TE in the preimplantation embryos. Therefore, it is of great importance for unveiling the interplays between H3K27me3 and DNA methylation involving in the restriction of developmental competence between embryonic cells and extraembryonic cells in post-implantation embryos.

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