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The Ultraconserved Long Noncoding RNA, T-UCstem1, controls proliferation and safeguards self-renewal of embryonic stem cells

ABSTRACT: The Ultraconserved Long Noncoding RNA, T-UCstem1, controls proliferation and safeguards self-renewal of embryonic stem cells

PROVIDER: PRJNA428221 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6434510_1.fastq.gz	Fastqsanger.gz
	SRR6434510_2.fastq.gz	Fastqsanger.gz
	SRR6434511_1.fastq.gz	Fastqsanger.gz
	SRR6434511_2.fastq.gz	Fastqsanger.gz
	SRR6434512_1.fastq.gz	Fastqsanger.gz

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The Ultraconserved Long Noncoding RNA, T-UCstem1, controls proliferation and safeguards self-renewal of embryonic stem cells

Project description:We reported RNA-seq transcriptome profiling of Control and T-UCstem1 KD ESCs (TBV2) grown in FBS/Lif and in optimal culture conditions (feeder cells/high density) using the Illumina HiSeq platform. Whole-genome expression revealed an enrichment in genes involved in regulation of cell proliferation, positive regulation of development and cell differentiation in T-UCstem1 depleted cells compared to N.T. A large number (~50%) of all the developmental regulatory genes that are up-regulated in T-UCstem1 KD ESCs are bivalent domains-associated genes. RNAseq data and validation both at RNA and protein level provide new evidences that T-UCstem1 is required to preserve self-renewal and transcriptional identity of ESCs.

2018-03-15 | GSE108662 | GEO

Asymmetric self-renewal associated (ASRA) genes

Project description:Cell lines geneticially engineered to undergo conditional asymmetric self-renewal were used to identify genes whose expression is asymmetric self-renewal associated (ASRA). Non-random sister chromatid segregation occurs concordantly with asymmetric self-renewal in these cell lines. Asymmetric self-renewal occurs when murine embryo fibroblasts that are otherwise p53-null are induced to express physiological levels of wildtype p53 protein (Asym). To distinguish p53-responsive genes that also require induction of asymmetric self renewal (i.e., ASRA genes) and/or non-random sister chromatid segregation for change, an additional control cell line, which continues to symmetrically self-renew (with random sister chromatid segregation) even when p53 is induced, was also compared (Symp53). This congenic cell line constitutively expresses the type II inosine monophosphate dehydrogenase (IMPDH II; the rate-limiting enzmye for guanine ribonucleotide biosynthesis) and, thereby, prevents p53-induced asymmetric self-renewal and non-random sister chromatid segregation. Three biological replicates of asymmetrically self-renewing cultures (Asym1-3) were compared with cultures that were symmetrically self-renewing - either because they did not express p53 (3 biological replicates, Sym1-3) or they expressed constitutive IMPDH II (i.e., not regulated by p53) as well as p53 (2 biological replicates, Symp53_1 and 2.)

2010-12-22 | E-GEOD-25334 | biostudies-arrayexpress

circular RNA Kat6b-e2 expression safeguards self-renewal and lineage differentiation of mouse embryonic stem cells

Project description:circular RNA Kat6b-e2 expression safeguards self-renewal and lineage differentiation of mouse embryonic stem cells

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HMCES safeguards genome integrity and long-term self-renewal of hematopoietic stem cells during stress responses

Project description:HMCES safeguards genome integrity and long-term self-renewal of hematopoietic stem cells during stress responses

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Asymmetric self-renewal associated (ASRA) genes

2010-12-22 | GSE25334 | GEO

Nuclear exosome targeting complex safeguards hematopoietic stem cell self-renewal and genomic integrity through resolving R loops

Project description:Nuclear exosome targeting complex safeguards hematopoietic stem cell self-renewal and genomic integrity through resolving R loops

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Long Noncoding RNA Moderates microRNA Activity to Maintain Self-Renewal in Embryonic Stem Cells

Project description:Of the thousands of long non-coding RNAs expressed in embryonic stem (ES) cells, few have known roles and fewer have been functionally implicated in the regulation of self-renewal and pluripotency or reprogramming somatic cells to the pluripotent state. In ES cells, Cyrano is a stably expressed long intergenic non-coding RNA with no previously assigned role. We demonstrate that Cyrano contributes to ES cell maintenance, as its depletion results in loss of hallmarks of self-renewal. Delineation of Cyrano's network through transcriptomics revealed widespread effects on signaling pathways and gene expression networks that contribute to ES cell maintenance. Cyrano shares unique sequence complementarity with the differentiation-associated microRNA, mir-7, and mir-7 overexpression reduces expression of a key self-renewal factor to a similar extent as Cyrano knockdown. This suggests that Cyrano functions to restrain the action of mir-7. Altogether, we provide a view into the multifaceted function of Cyrano in ES cell maintenance.

2017-04-28 | GSE98297 | GEO

MacroH2A2 modulates the self-renewal of glioblastoma cells

Project description:Self-renewal is a crucial property of glioblastoma cells and is enabled by the choreographed function of chromatin regulators and transcription factors. Identifying targetable epigenetic mechanisms of self-renewal could represent an important step toward developing new and effective treatments for this universally lethal cancer. Here we uncover a targetable epigenetic axis of self-renewal mediated by the histone variant macroH2A2.

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Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L

Project description:The transition between quiescence and activation in neural stem and progenitor cells (NSPCs) is coupled to reversible changes in energy metabolism with key implications for life-long NSPC self-renewal and neurogenesis. How this metabolic plasticity is ensured between NSPC activity states is unclear. We find that a state-specific rewiring of the mitochondrial proteome by the i-AAA peptidase YME1L is required to preserve NSPC self-renewal. YME1L controls the abundance of numerous mitochondrial substrates in quiescent NSPCs, and its deletion activates a differentiation program characterized by broad metabolic changes causing the irreversible shift away from a fatty acid oxidation-dependent state. Conditional Yme1l deletion in adult NSPCs in vivo results in defective self-renewal and premature differentiation, ultimately leading to NSPC pool depletion. Our results disclose an important role for YME1L in coordinating the switch between metabolic states of NSPCs and suggest that NSPC fate is regulated by compartmentalized changes in protein network dynamics.

2022-02-10 | PXD030995 | Pride

circular RNA Kat6b-e2 expression safeguards self-renewal and lineage differentiation of mouse embryonic stem cells

Project description:Circular RNA has been reported to be dynamically expressed during embryonic development and regulates human embryonic stem cells (hESCs), but the identification and regulation of functional circular RNA in mouse embryonic stem cells (mESC) remains unclear. Here we found over 1,000 circular RNAs in different mESC states. One of these, circular RNA Kat6b-exon2 (circKat6b-e2), was significantly overexpressed in mESCs. Furthermore, short-hair RNA (shRNA) mediated knockdown of circKat6b-e2 expression significantly inhibited mESC self-renewal and EB differentiation. The transcriptome also revealed that circKat6b-e2 is required to ensure the differentiation of the mESC lineage. Finally, we also found that more Alu elements surrounding circKat6b-e2 were necessary factors for its expression. Conclusions: our study shows that Alu element-dependent expression of circKat6b-e2 mediates mESC self-renewal and lineage differentiation.

2022-08-28 | GSE211667 | GEO

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