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Effect of depletion of Hp1α (Cbx5) and Hp1β (Cbx1) on gene expression of mouse embryonic stem cells (mESCs)

ABSTRACT: Effect of depletion of Hp1α (Cbx5) and Hp1β (Cbx1) on gene expression of mouse embryonic stem cells (mESCs)

PROVIDER: PRJNA833445 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18976342_1.fastq.gz	Fastqsanger.gz
	SRR18976342_2.fastq.gz	Fastqsanger.gz
	SRR18976343_1.fastq.gz	Fastqsanger.gz
	SRR18976343_2.fastq.gz	Fastqsanger.gz
	SRR18976344_1.fastq.gz	Fastqsanger.gz

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Effect of depletion of Hp1α (Cbx5) and Hp1β (Cbx1) on gene expression of mouse embryonic stem cells (mESCs)

Project description:To investigate the function of HP1α and HP1β proteins in the regulation of heterochromatin in mESCs, we isolated blastocysts from matings of mice homozygous for Hp1βF/F; Hp1αF/F in a single well of a 96-well plate in ESC medium. After 2 days, when blastocysts hatched, they were trypsinized and cells were seeded in the same well for other 2 days. Expanded mESC clones were further tested for their genotype by PCR. A single clone of Hp1βF/F; Hp1αF/F was transfected with either pCAG-Cre-GFP or pCAG-GFP as a control. GFP positive cells were sorted by flow cytometry and seeded into 10 cm plates. Individual clones were isolated and expanded. Deletion of Hp1β or Hp1α floxed alleles in pCAG-Cre-GFP transfected clones was tested by Western Blotting with appropriate antibodies.

2023-01-25 | GSE201907 | GEO

HP1, H3-K27me3, and H3-K9me3 Cut & Tag of Het (Cbx1+/+, Cbx3+/+, Cbx5+/-) and TKO (Cbx1-/-, Cbx3-/-, Cbx5-/-) bipotential mouse embryonic liver (BMEL) cells

Project description:HP1, H3-K27me3, and H3-K9me3 Cut & Tag of Het (Cbx1+/+, Cbx3+/+, Cbx5+/-) and TKO (Cbx1-/-, Cbx3-/-, Cbx5-/-) bipotential mouse embryonic liver (BMEL) cells

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The distribution of HP1α in the genome of intrahepatic cholangiocarcinoma cells

Project description:Heterochromatin Protein 1α (HP1α, encoded by the CBX5 gene) is one of the most important HP1 family members and is a nonhistone chromosomal proteins involved in transcriptional silencing via heterochromatin formation and structural maintenance. Many studies have shown that the distribution of HP1α on polytene chromosomes is not restricted to the chromocenters or telomeres. HP1α binds to chromatin mainly through direct interactions with modified histones, especially trimethylated H3K9 (H3K9me3), through the Chromo domain, and by interactions with other proteins through the Chromo shadow domain. In cancerous lesions, HP1α is involved in the regulation of malignant behaviors, such as cell proliferation and cell cycle progression. To study the distribution of HP1α in the genome of intrahepatic cholangiocarcinoma cells, CUT & Tag was performed. We found that HP1α was significantly distributed in the promoter region of proliferation-related encoding genes. No peaks were detected in the normal control sample.

2025-01-20 | GSE252096 | GEO

ChIP-MS of HP1-beta (CBX1) and ubiquitylome of KAP1 (TRIM28) in mESCs

Project description:Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β-/- embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β-/- and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1ΔRing cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.

2021-09-24 | PXD025053 | Pride

HP1β dependent phase separation regulates embryonic stem cells exit from naïve pluripotent state

Project description:Liquid-liquid phase separation has drawn great attention as a physical process that mediates the formation of membraneless organelles in cells to coordinate biological reactions in space and time. Previously, it was proposed that the formation of phase-separated droplets is a unique property of HP1α. Here, we show that HP1β, but not HP1α and HP1ɤ, forms nucleosome dependent phase separated droplets. We demonstrate that H3K9me3 is required for HP1β dependent phase separation. Importantly, HP1β dependent phase separation regulates heterochromatin formation, thus controlling embryonic stem cells differentiation. In response to pluripotency exit, HP1β is phosphorylated at serine 89 recruiting KAP1, a pluripotency regulator, and sequestering it in the heterochromatin compartment. This induces changes in the level of pluripotency factors and triggers pluripotency exit. We propose that such a trapping mechanism creates a fast and dynamic mode of remote control of gene expression to regulate cell fate decisions solely based on membraneless organelles.

2022-05-01 | E-MTAB-8329 | biostudies-arrayexpress

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Project description:ChIP experiment against anti-FLAG in SUNE1 cells trasfected with FLAG-CBX1 plasmid.

2023-01-04 | GSE201232 | GEO

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. ChIP-Seq of HP1β in mouse embryonic stem cells.

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

BRD4 represses CBX5

Project description:BRD4 is amplified and/or up-regiulated in a subset of ovarian cancer which correlates with a poor survival siRNA sensitization screens in the presence of CHK1 inhibitor, LY2606368, identify BRD4 as a therapeutic target in ovarian cancer. BRD4 suppression by either siRNA or using JQ1 increases CBX5 expression

2016-05-01 | GSE78704 | GEO

HP1β 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.

2015-08-02 | GSE65121 | GEO

A heterochromatin gene signature unveils HP1α mediating neuroendocrine prostate cancer development and aggressiveness

Project description:Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer (PCa) with hyperchromatic nuclei being a distinguishing histopathological feature. Here we show that, underlying this distinct nuclear structure, heterochromatin related genes are significantly enriched in NEPC. Among them, heterochromatin protein 1α (HP1α) expression is increased early in NE transdifferentiation and is consistently elevated in clinical NEPC samples. Functional studies showed that HP1α knockdown attenuates NEPC tumor growth by inhibiting proliferation and survival. Its ectopic expression significantly promotes NE transdifferentiation in adenocarcinoma cells subjected to androgen deprivation treatment. To identify mechanisms underlying the function of HP1α involved in NEPC cell proliferation and adenocarcinoma cell NE transdifferentiation, we analyzed gene expression profiles from stable NEPC cell lines with control or HP1α knockdown, and adenocarcinoma cell lines with control or HP1α overexpression, respectively.

2018-01-22 | GSE105033 | GEO

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