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HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [expression]

ABSTRACT: We used microarrays to identify the gene expression changes in Cbx1-/- (HP1beta) knockout embryonic stem cells (ESCs) and Cbx5-/- (HP1alpha) knockout ESCs compared to WT ESCs and in embryoid bodies (EBs) differentiated from those three ESC types.

ORGANISM(S): Mus musculus

PROVIDER: GSE65121 | GEO | 2015/08/02

SECONDARY ACCESSION(S): PRJNA273153

REPOSITORIES: GEO

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HP1? has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [expression]

Project description:We used microarrays to identify the gene expression changes in Cbx1-/- (HP1beta) knockout embryonic stem cells (ESCs) and Cbx5-/- (HP1alpha) knockout ESCs compared to WT ESCs and in embryoid bodies (EBs) differentiated from those three ESC types. ESCs were grown and the pluripotent SSEA1-positive cells from all ESC types using MACS were sorted and harvested or sorted and differentiated into EBs. Total RNA from all samples was extracted.

2015-08-02 | E-GEOD-65121 | biostudies-arrayexpress

HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [ChIP-seq]

Project description:In recent years, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, although the role of the major heterochromatin proteins in pluripotency remains largely unknown. Here we identify heterochromatin protein 1-beta (HP1β) to be differentially localized and associated with chromatin in pluripotent and differentiated cells, to be essential for proper ESC differentiation as well as for the maintenance of the pluripotent state. Microscopy analysis supported by biochemical fractionations and chromatin immunoprecipitation (ChIP) experiments demonstrate that unlike its prominent localization in heterochromatic chromocenters in differentiated cells, HP1β is diffuse in the ESC nucleoplasm, poorly bound to chromatin, and highly expressed. The fraction of HP1β that does associate with chromatin in ESCs is highly enriched in genic regions. HP1β-knockout ESCs but not HP1α knockout ESCs exhibit a loss of the morphological and proliferative characteristics of embryonic pluripotent cells. HP1β depletion in ESCs results in reduced expression of pluripotency factors and aberrant differentiation. In contrast, HP1β depletion in differentiated cells perturbs the maintenance of differentiation, and facilitates reprogramming to induced pluripotent stem cells. Our results demonstrate a dual role for HP1β, in ESCs it is essential for pluripotency maintenance, and in differentiated cells for proper differentiation.

2015-08-02 | GSE64946 | GEO

HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [ChIP-seq]

2015-08-02 | E-GEOD-64946 | biostudies-arrayexpress

Expression data from control (F/F) and Snai1 knockout (KO) embryoid body (EB) and teratoma ™

Project description:Snai1 is a master factor of epithelial to mesenchymal transitioin (EMT), however, its role in embryonic stem cell (ESC) differentiation and lineage commitment remains undefined. We used microarrays to compare the global programme of gene expression between control and Snai1 knockout ESCs-derived EB and teratoma. For EBs, control and Snai1 knockout ESCs were cultured as embryoid bodies in spotaneous differentiation media, RNA of 5 days EBs were collected for Affymetrix microarrays. For teratomas, control and Snai1 knockout ESCs were injected into nude mice to form teratomas. RNA of 6 weeks were collected for Affymetrix microarrays.

2013-12-10 | E-GEOD-53106 | biostudies-arrayexpress

Loss of Tet enzymes compromises proper differentiation of embryonic stem cells

Project description:Tet enzymes (Tet1/2/3) convert 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and are dynamically expressed in various embryonic and adult cell types. While loss of individual Tet enzymes or combined deficiency of Tet1/2 allows for embryogenesis, the effect of complete loss of Tet activity and 5hmC marks in development is not established. We have generated Tet1/2/3 triple knockout (TKO) mouse embryonic stem cells (ESCs) and examined their developmental potential. Combined deficiency of all three Tets depleted 5hmC and impaired ESC differentiation as seen in poorly differentiated TKO embryoid bodies (EBs) and teratomas. Consistent with impaired differentiation, TKO-ESCs contributed poorly to chimeric embryos and could not support embryonic development. Global gene expression and methylome analyses of TKO-EBs revealed promoter hypermethylation and deregulation of genes implicated in embryonic development and differentiation. These findings suggest a requirement for Tet- and 5hmC-mediated DNA demethylation in proper regulation of gene expression during differentiation of ESCs and development. To quantify global gene expression in differentiating embryoid bodies (EBs) derived from wild type (WT) and Tet triple knockout (TKO), TKO and WT mouse embryonic stem cells (ESCs) were differentiated in vitro to EBs and cultured for 10 days. RNA was extracted using Qiagen RNeasy kit and subjected to microarray analysis. Global gene expression profile of two technical replicas of WT embryoid bodies (2 samples in total) was compared to two technical replicas of two independent TKO embryoid bodies (4 TKO samples in total).

2014-04-14 | E-GEOD-55574 | biostudies-arrayexpress

Expression data of control (F/F) and Snai1 knockout (KO) Flk1+/- cells

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2013-12-10 | E-GEOD-53108 | biostudies-arrayexpress

Mouse_embryoid Body_Retinoic acid treatment

Project description:S6K1 Knockout mice has a lean phenotype and resitant to a High Fat Diet-induced obesity (Um S.H., Nature, 2004). Adipocyte differentiation consists of two step, first, commitment from stem cell to adipocyte progenitors and second, terminal differentiation from adipocyte progenitors to mature adipocyte. We studied S6K1-dependent gene expression regulation in early stage of commitment by employing ES cell(ESC)-Embryoid Bodies(EBs) differentiation model. We established stable ES cell lines infected with either control non-silencing shRNA (shNS) or S6K1 targetting shRNA (shS6K1). Each sample was treated with retinoic acid for 3 days to induce adipogenesis, then gene expression profile was analyzed employing microarrays and up-regulated and down-regulated genes were selected for analysis. Mouse Embryoid Bodies (approximately 1000 EBs per sample) were treated with retinoic acid (1ÂµM) for 3 days then collected for RNA extraction and hybridization on Affimetrix microarray. Two biological replicates were each performed for EBs prepared from either shNS ESCs or shS6K1 ESCs.

2010-05-14 | E-GEOD-20349 | biostudies-arrayexpress

In vitro modeling of primordial germ cell development

Project description:Transgenic StellaGFP ESCs were used to derive primordial germ cells during embryoid body (EB) differentiation, and microarry analysis used to compared FACS sorted Stella-positive cells of day 7 Ebs with the parental ESCs and Stella-negative cells of day 7 Ebs. Keywords: in vitro, primordial germ cells, embryonic stem cells, stella

2009-06-22 | GSE7948 | GEO

RNA Sequencing Data in differentiating mouse embryonic stem cells

Project description:ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies (EBs) were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were induced with Tamoxifen at day 4 and harvested at day 7.

2016-11-14 | GSE80166 | GEO

RNA Seq to identify novel transcripts originating from orphan CGIs

Project description:To identify novel transcripts originating from orphan CGIs we isolated RNA from undifferentiated embryonic stem cells (ESCs), ESCs differentiated into embryoid bodies (EBs), and ESCs differentiated into neuronal cells; we also used RNA from mature male mouse brain. RNA Seq data were visually analysed for transcripts originating from orphan CGIs.

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