Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of control siRNA, p150 siRNA and p60 siRNA transfected mES cells

ABSTRACT: Totipotent cells that resemble 2-cell stage embryos (2C-like cells) can arise with a very low frequency in ES cell cultures. Here we show that totipotent-like cells can be induced in vitro through the down-regulation of the chromatin assembly activity of CAF-1. Endogenous retroviruses and 2-cell stage specific genes are among the highest upregulated genes upon CAF-1 knockdown and the emerging totipotent-like cells exhibit the molecular characteristics of endogenous 2C-like cells and 2-cell embryos. CAF-1 depletion leads to increased accessibility at MERVL elements and to the up-regulation of neighbouring genes, thereby generating a transcriptional profile similar to that of 2-cell stage embryos.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Juan Vaquerizas

PROVIDER: E-MTAB-2684 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly.

Ishiuchi Takashi T Enriquez-Gasca Rocio R Mizutani Eiji E Bošković Ana A Ziegler-Birling Celine C Rodriguez-Terrones Diego D Wakayama Teruhiko T Vaquerizas Juan M JM Torres-Padilla Maria-Elena ME

Nature structural & molecular biology 20150803 9

Cellular plasticity is essential for early embryonic cells. Unlike pluripotent cells, which form embryonic tissues, totipotent cells can generate a complete organism including embryonic and extraembryonic tissues. Cells resembling 2-cell-stage embryos (2C-like cells) arise at very low frequency in embryonic stem (ES) cell cultures. Although induced reprogramming to pluripotency is well established, totipotent cells remain poorly characterized, and whether reprogramming to totipotency is possible ...[more]

PMID: 26237512

Similar Datasets

Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons [RNA-seq]

Project description:During the development in mouse early embryos, a subset of retrotransposons and genes are transiently expressed in the totipotent 2-cell embryos. These 2-cell-embryo-asscoiated (referred to as 2C) transcripts rapidly shut down their expression beyond the late 2-cell stage of embryos, and this timely shutdown governs the embryo to exit from the 2-cell stage. However, mechanisms regulating this wave of shutdown are not fully understood. In this study, we established a novel connection between lysosomal catabolic activity and 2C transcripts in regulating the exit of totipotent 2-cell state by using both in vitro 2-cell-like cells model and mouse embryos. Our results showed that the activation of lysosomal catabolism in mouse embryos governed the embryo to exit from the 2-cell state by suppressing the expression of 2C transcripts. Mechanistically, we found that lysosomal catabolic activity modulated 2C transcripts by inactivating transcriptional factors Tfe3/Tfeb and abolishing their transcriptional activation on 2C retrotransposons, MERVL/MT2-Mm. Collectively, our study elucidates the function of lysosomal activity in orchestrating transcriptomic landscape and early development in mouse embryos and reveals an unanticipated layer of transcriptional control on early-embryonic retrotransposons from lysosomal signaling.

2024-08-25 | GSE247082 | GEO

Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons [CUT&Tag]

2024-08-25 | GSE247081 | GEO

NR5A2 connects genome activation to the first lineage segregation in totipotent embryos

Project description:Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to inner cell mass (ICM), where pluripotent epiblast arises, and extraembryonic trophectoderm. While much has been learned about pluripotency regulation, how ZGA is connected to the first lineage segregation in early embryos remains elusive. Here, we investigated the role of nuclear receptor transcription factors (NR TFs), whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. We found NR5A2, an NR TF highly induced upon ZGA, is required for early development. Genome-wide chromatin binding in 2C and 8C embryos showed NR5A2 bound cis-regulatory elements which strongly enrich B1 elements where its motif is embedded. RNA-seq showed while the zygotic genome was largely activated at the 2C stage, 4-8C-specific gene activation was substantially impaired in Nr5a2 KD embryos. At the 8C stage, NR5A2 preferentially regulated its targets including a subset of early ICM genes. Consistently, NR5A2 was required for opening 8C-specific binding sites. Interestingly, while NR5A2’s 2C-binding sites are largely closed in blastocyst, 8C-specific binding sites tend to stay open and are bound by master pluripotency TFs (NANOG, SOX2, and OCT4) in blastocyst or ESC. Further analyses showed NR5A2 regulates early ICM genes at the 8C stage, master pluripotency TFs regulate both early and late ICM genes at later stages. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that connects ZGA to the first lineage segregation in early mouse development.

2023-10-12 | GSE229740 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [ATAC-seq 2]

Project description:Totipotent cells have more robust developmental potency than any other cell types, giving rise to both embryonic and extraembryonic tissues. Stable totipotent cultures and deciphering the principles of totipotency regulation would be invaluable to understand cell plasticity and lineage segregation in early development. Our approach of remodeling the pericentromeric heterochromatin and re-establishing the totipotency-specific broad H3K4me3 domains promotes the pluri-to-totipotency transition. Our protocol establishes a closer match of mouse 2-cell (2C) embryos than any other 2C-like cells. These totipotent-like stem cells (TLSCs) are stable in culture and possess unique molecular features of the mouse 2C embryo. Functionally, TLSCs are competent for germline transmission and give rise to both embryonic and extraembryonic lineages at high frequency. Therefore, TLSCs represent a highly valuable cell type for studies of totipotency and embryology.

2022-02-11 | GSE185034 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [CUT&Tag 2]

2022-02-11 | GSE185032 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [RNA-seq 2]

2022-02-11 | GSE185030 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [ATAC-seq]

2022-02-11 | GSE166215 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [CUT&Tag]

2022-02-11 | GSE166210 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [ChIP-seq]

2022-02-11 | GSE166208 | GEO

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [RNA-seq]