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Next-Generation Sequencing Facilitates Quantitative Analysis of WT, Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- Embryonic Stem Cells Transcriptomes

ABSTRACT: Next-Generation Sequencing Facilitates Quantitative Analysis of WT, Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- Embryonic Stem Cells Transcriptomes

PROVIDER: PRJNA761488 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15792418_1.fastq.gz	Fastqsanger.gz
	SRR15792418_2.fastq.gz	Fastqsanger.gz
	SRR15792420_1.fastq.gz	Fastqsanger.gz
	SRR15792420_2.fastq.gz	Fastqsanger.gz
	SRR15792422_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Next-Generation Sequencing Facilitates Quantitative Analysis of WT, Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- Embryonic Stem Cells Transcriptomes

Project description:Polycomb repressive complexes (PRC) are epigenetic transcriptional repressors by establishing facultative heterochromatin repressive domains and play an essential role in numerous developmental processes. PRC1, which contains the E3 ligases RING1A/B and deposits H2AK119ub, forms six biochemically subcomplexes (PRC1.1-PRC1.6) based on the assembled PCGF protein (PCGF1–PCGF6), and has been involved in the maintenance of embryonic stem (ES) cell state. More recent evidence indicates that PCGF family participates in the self-renewal and pluripotent maintenance. However, it is still enigmatic that how the PCGF family engaged in the controlling process. Here, we generate the Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- ES cells using CRISPR/Cas9 technique and CRE-LoxP recombination system to discover the central determinants in PCGF family-related biological process.

2022-09-01 | GSE183646 | GEO

Disruption of PRC1 Components RING1A and RING1B Promotes Angiogenesis via Relieving BMP4 Repression [CUT&Tag]

Project description:Angiogenesis is crucial for maintaining tissue homeostasis and responding to injury and disease. Epigenetic mechanisms have been elucidated to regulate the expression of pro-angiogenic factors and modulate angiogenesis. The Polycomb repressive complex 1 (PRC1) is a key epigenetic repressive complex that regulates multiple biological functions. Within this complex, RING1A and RING1B, which serve as the E3 ubiquitin ligases for PRC1, contribute to the monoubiquitylation of histone H2A on Lysine 119 (H2AK119ub), thereby repressing gene transcription. However, the role of RING1A and RING1B in regulating angiogenesis has remained elusive. In this study, we demonstrate that RING1A and RING1B suppress angiogenic capacity in vitro, although they do not inhibit migration and proliferation in endothelial cells (ECs). Furthermore, by integrating RNA sequencing data from RING1A knockdown or RING1B knockdown ECs with CUT&Tag assay results for RING1A, RING1B, and H2AK119ub in ECs, we have identified that PRC1 inhibits angiogenesis by repressing BMP4 expression, a pro-angiogenic factor known to regulate angiogenesis. Additionally, we verify that the knockdown of RING1A and RING1B enhances angiogenesis in vivo, which may provide a new therapeutic target for angiogenesis-related diseases.

2025-07-24 | GSE281870 | GEO

Disruption of PRC1 Components RING1A and RING1B Promotes Angiogenesis via Relieving BMP4 Repression [RNA-Seq]

2025-07-24 | GSE281872 | GEO

ChIP-on-chip analysis of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells

Project description:ChIP-on-chip analysis was carried out to determine targets of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells.

2012-06-06 | GSE38504 | GEO

Ring1A and Ring1B maintain murine MOZ-TIF2 AML stem cells by inhibiting expression of Glis2

Project description:Eradication of chemotherapy-resistant leukemia stem cells is expected to improve treatment outcomes in patients with acute myelogenous leukemia (AML). In a mouse model of AML expressing the MOZ-TIF2 fusion, we found that Ring1A and Ring1B, components of Polycomb repressive complex 1, play crucial roles in maintaining AML stem cells. Deletion of Ring1A and Ring1B (Ring1A/B) from MOZ-TIF2 AML cells diminished self-renewal capacity and induced the expression of numerous genes including Gli-similar 2 (Glis2). Overexpression of Glis2 caused MOZ-TIF2 AML cells to differentiate into mature cells, whereas Glis2 knockdown in Ring1A/B-deficient MOZ-TIF2 cells inhibited differentiation. Thus, Ring1A/B regulates and maintains AML stem cells in part by repressing Glis2 expression, which promotes their differentiation. These findings provide new insights into the mechanism of AML stem cell homeostasis and reveal novel targets for cancer stem cell therapy.

2017-01-06 | GSE93214 | GEO

Expression data from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing either of mock, WT or mutant Ring1B construct before or after OHT treatment

Project description:We used microarrays to investigate the restoration of repression of PRC1 target gene expression in Ring1A/B-dKO ES cells stably expressing either of mock, WT or mutant Ring1B construct.

2012-06-11 | GSE38224 | GEO

Transcription profiling of mouse Ring1B single and Ring1A/B double knockout cells shows Ring1B interacts with Oct4.

Project description:The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5. PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8. PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4. We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome. Experiment Overall Design: We observed gene expression of Ring1B single and Ring1A/B double KO cells using Affymetrix chip: MOE 430 2.0. Experiment Overall Design: Because constitutive Ring1A/B-dKO cells can not be maintained we generated conditional KO cells with OHT.

2008-04-07 | E-GEOD-10476 | biostudies-arrayexpress

Transcriptommic profiling of hematopoietic progenitor cells following PCGF1 loss

Project description:Polycomb proteins are epigenetic regulators important for cell fate decision and maintenance. Here we show that PCGF1, one of components of Polycomb repressive complex (PRC) 1 is important for the differentiation of hematopoietic stem/progenitor cells (HSPCs) towards lymphoid lineage. The deletion of Pcgf1 in HSPCs lead to severe defects in B cell development with an expansion of myeloid progenitors. The blockade of B cell differentiation occurred at the lymphoid-primed multipotent progenitor (LMPP) stage. Chromatin immunoprecipitation followed by DNA sequencing analysis of normal LMPP-like cells demonstrated that PCGF1 colocalized with RING1A/B and PRC2. Upon deletion of Pcgf1, we found dramatic decline of H3K27me3 levels, resulting in de-repression of target genes. Strikingly, the occupancy of RING1A/B, PRC2 and monoubiquitination of histone H2A at lysin 119 on the target loci was not affected. These results demonstrate that the PCGF1 safeguards the immune system development by directly regulating the PRC2-mediated H3K27me3 levels.

2022-10-19 | GSE141523 | GEO

Gene regulation by PCGF1 in hematopoietic progenitor cells [ChIP, MNaseSeq]

2022-10-19 | GSE141559 | GEO

H3K4me1 and H3K27ac ChIP-seq in Ring1a KO and Ring1a/b dKO mouse ES cells

Project description:H3K4me1 (ab8895 Abcam) and H3K27ac (ab4729 Abcam) antibodies were used for ChIP-seq in Ring1a-/- mouse ES cells and after 48h tamoxifen treatment in conditional knock-out of Ring1b in the Ring1a -/- background.

2015-08-01 | E-MTAB-3156 | biostudies-arrayexpress

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