Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells

ABSTRACT: Embryonic stem cell (ESC) fate decisions are regulated by a complex molecular circuitry that requires tightly coordinated gene expression regulations at multiple levels from chromatin organization to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis. However, the molecular mechanisms underlying the regulation of these pathways remain largely unknown to date. Here, we analyzed the expression of over 300 genes involved in ribosome biogenesis between self-renewing and differentiated mouse ESCs. We identified RSL24D1 as highly expressed in multiple mouse pluripotent stem cell models and showed that its expression profile is conserved in human ESCs. RSL24D1 is associated with nuclear pre-ribosomes and is required for the maturation and the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion resulted in a significant modification of ESC’s proteome by impairing global translation, particularly of key pluripotency factors, including POU5F1 and NANOG, as well as components of the polycomb repressive complex 2 (PRC2). Consistently, while having a moderate impact on lineage commitment and cell differentiation, RSL24D1 depletion significantly altered mouse ESC self-renewal and proliferation, a phenotype largely alleviated by RSL24D1 knockdown rescue. Taken together, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-dependant developmental programs, which concertedly dictate ESC homeostasis.

ORGANISM(S): Mus musculus

PROVIDER: GSE218290 | GEO | 2023/01/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

MS-based quantitative proteomic analysis of embryonic stem cells with normal and reduced expression of Rsl24d1.

Project description:Embryonic stem cell (ESC) fate decisions are regulated by a complex molecular circuitry that requires tight and coordinated gene expression regulations at multiple levels from chromatin organization to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis. However, the molecular mechanisms underlying the regulation of these pathways remain largely unknown to date. Here, we analyzed the expression, in mouse ESCs, of over 300 genes involved in ribosome biogenesis and we identified RSL24D1 as the most differentially expressed between self-renewing and differentiated ESCs. RSL24D1 is highly expressed in multiple mouse pluripotent stem cell models and its expression profile is conserved in human ESCs. RSL24D1 is associated with nuclear pre-ribosomes and is required for the maturation and the synthesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors, including POU5F1 and NANOG, as well as components of the polycomb repressive complex 2 (PRC2). Consistently, RSL24D1 is required for mouse ESC self-renewal and proliferation. Taken together, we show that RSL24D1-dependant ribosome biogenesis is required to both sustain the expression of pluripotent transcriptional programs and silence developmental programs, which concertedly dictate ESC homeostasis.

2023-01-10 | PXD030497 | Pride

RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells.

2024-09-06 | GSE183586 | GEO

Integrative proteomics reveals a protective role of PRC2 for the ground state pluripotent epigenome

Project description:The ground state of pluripotency is defined as a basal proliferative state free of epigenetic restriction, represented by mouse embryonic stem cells (ESCs) cultured with two kinase inhibitors (so-called “2i”). Through comparison with serum-grown ESCs, we identify epigenetic features characterizing 2i ESCs by proteome profiling of chromatin including post-translational histone modifications. The most prominent difference is H3K27me3 and its enzymatic writer complex PRC2 that are highly abundant on eu- and heterochromatin in 2i ESCs, with H3K27me3 redistributing outside canonical PRC2 targets in a CpG-dependent fashion. Using PRC2-deficient 2i ESCs, we identify epigenetic crosstalk with H3K27me3, including significant increases in H4 acetylation and DNA methylation. This suggests that the unique H3K27me3 configuration protects 2i ESCs from preparation to lineage priming. Interestingly, removal of DNA methylation in PRC2-deficient 2i ESCs lacking H3K27me3 using 5-azacytidine hardly affected ESC viability and transcriptome, showing that ESCs are independent of both major repressive epigenetic marks.

2018-11-21 | PXD007154 | Pride

Polycomb-like 2 associates with PRC2 and is required for mouse embryonic stem cell

Project description:Polycomb group (PcG) proteins are highly conserved epigenetic transcriptional repressors important for the control of numerous developmental gene expression programs and have recently been implicated in the modulation of embryonic stem cell (ESC) identity. We identified the PcG protein PCL2 (polycomb-like 2) in a genome-wide screen for novel regulators of self-renewal and pluripotency and predicted that it would play an important role in mouse ESC fate determination. Using multiple biochemical strategies, we provide evidence that PCL2 is a novel Polycomb Repressive Complex 2 (PRC2)-associated protein in mouse ESCs. Knockdown of Pcl2 in ESCs resulted in heightened self-renewal characteristics, defects in differentiation and altered patterns of histone methylation. Through integration of global gene expression and promoter occupancy analyses of both PCL2 and PRC2 components EZH2 and SUZ12, we have predicted PCL2 target genes and formulated regulatory networks describing the role of PCL2 both in modulating transcription of ESC self-renewal genes in undifferentiated ESCs as well as developmental regulators during early commitment and differentiation. Cells were stably expressing Pcl2 shRNA or shRNA mismatch control sequences. Hybridizations of three biological replicates for both the control and Pcl2 shRNA clone were performed.

2010-02-22 | E-GEOD-16364 | biostudies-arrayexpress

Polycomb-like 2 associates with PRC2 and is required for mouse embryonic stem cell

2010-02-05 | GSE16364 | GEO

HEB associates with PRC2 and SMAD2/3 to regulate developmental fates [ChIP-Seq]

Project description:We report the interaction between HEB and PRC2 components in mouse embryonic stem cells (ESCs) ChIP-Seq of HEB and SMAD2/3 in mouse ESC and derived endoderm

2015-06-30 | E-GEOD-53233 | biostudies-arrayexpress

NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells

Project description:The Nucleosome Remodeling and Deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. Yet little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). The genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as a novel, ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD interacting protein which regulates genome-wide NuRD binding and cellular differentiation.

2018-10-11 | PXD010512 | Pride

ZZZ3 protects human embryonic stem cells from nucleolar stress by boosting mTOR/ribosome pathway

Project description:Embryonic stem cells (ESCs) are defined as stem cells with self-renewing and differentiation capabilities. These unique properties are tightly regulated and controlled by complex genetic and molecular mechanisms whose understanding is essential for both basic and translational research. A large number of existing studies in the broader literature have mostly focused on understanding the molecular mechanisms governing pluripotency and differentiation of ESCs, while the regulation of proliferation has received comparably less attention. Proliferation is a fundamental aspect of stem cell biology and despite its importance, the intricate mechanisms governing proliferation in human ESCs are not fully understood. In mouse ESCs, pluripotency and proliferation can be independent processes meaning that it is possible for mouse ESCs to maintain their pluripotent state without actively proliferating. Ribosome biogenesis and translation have emerged as critical pathways that play essential roles in regulating stem cell homeostasis influencing cell growth and division rates. Here, we aim at investigating the role of ZZZ3 (Zinc Finger ZZ-Type Containing 3) in human ESCs homeostasis. ZZZ3 is expressed in both mouse and human pluripotent stem cells and regulates genes encoding ribosomal proteins (RPGs). However, its precise function in human pluripotent stem cells (PSCs) still remains elusive. Interestingly, we found that knockdown of ZZZ3 strongly decreases ribosome biogenesis, translation, and mTOR signaling leading to nucleolar stress and significant reduction of cell proliferation. This process occurs without affecting pluripotency, suggesting that ZZZ3-depleted ESCs enter a dormant-like state and that proliferation and pluripotency can be uncoupled also in human ESCs. Our study shows that ZZZ3 controls ribosome biogenesis, translation, and proliferation of stem cells and protects hESCs from nucleolar stress.

2024-05-16 | GSE242489 | GEO

Polycomb-like 3 is a PRC2 component that supports embryonic stem cell self-renewal

Project description:Polycomb repressive complex 2 (PRC2) trimethylates lysine 27 of histone H3 (H3K27me3), which regulates gene expression and controls diverse biological transitions in development, embryonic stem cell (ESC) differentiation, and cancer. Here we show that Polycomb-like 3 (Pcl3) is a component of PRC2 that promotes H3K27 trimethylation in ESCs. Chromatin immunoprecipitation and sequencing (ChIP-seq) revealed that Pcl3 co-localizes and recruits Suz12 to CpG islands. Depletion of Pcl3 decreased Suz12 binding at over 60% of PRC2 targets, including many bivalent genes. Pcl3 promotes ESC self-renewal as knockdown of Pcl3 increased spontaneous differentiation. However, Pcl3 does not affect ESC pluripotency as teratomas derived from Pcl3-depleted ESCs were able to form all three germ layers. Mutation of conserved residues within the Pcl3 TUDOR domain, a domain that recognizes methylated histones, compromises H3K27me3, suggesting that the TUDOR domain of Pcl3 is crucial for function. Thus, Pcl3 is a component of PRC2 critical for histone methylation and PRC2 recruitment. We reverted a Suz12 gene trap (Suz12Gt/+) allele generated in a mouse ESC line to produce an allele that re-expresses Suz12 but that contains a loxP targeting site (Suz12Rev/+). Using a modified Floxin shuttle vector, we inserted an exon encoding amino acids 277-741 of Suz12 fused to a carboxy-terminal 6xHis-3xFlag TAP tag. The resultant allele (Suz12Suz12TAP/+) expresses the full-length TAP-tagged Suz12 from the endogenous locus. We then reduced Pcl3 expression by siRNA or shRNA. Finally, we performed ChIP-Seq using the Flag tag of Suz12Suz12TAP/+ cells expressing either Pcl3 or control shRNA. To perform Pcl3 ChIP-seq, we created ESC clones expressing Pcl3-shRNAs and a TAP-tagged Pcl3 not recognized by the Pcl3-shRNAs.

2012-03-15 | E-GEOD-28325 | biostudies-arrayexpress

Polycomb-like 3 is a PRC2 component that supports embryonic stem cell self-renewal

2012-03-15 | GSE28325 | GEO