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Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

ABSTRACT: Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

PROVIDER: PRJNA895350 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22077658.fastq.gz	Fastqsanger.gz
	SRR22077659.fastq.gz	Fastqsanger.gz
	SRR22077660.fastq.gz	Fastqsanger.gz
	SRR22077661.fastq.gz	Fastqsanger.gz
	SRR22077662.fastq.gz	Fastqsanger.gz

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Similar Datasets

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression

Project description:Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression

| PRJNA895357 | ENA

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

Project description:The temporal order of DNA replication along chromosomes is reorganized in the context of cell differentiation and disease states and is thought to reflect transcriptional competence of the genome. During differentiation of mouse 3T3-L1 cells into adipocytes, cells undergo one or two rounds of cell division called mitotic clonal expansion (MCE). MCE is an essential step for adipogenesis; however, little is known about the regulation of DNA replication during this period. Here, we performed genome-wide mapping of replication timing (RT) in mouse 3T3-L1 cells before and during MCE and identified a number of chromosomal regions shifting toward either earlier or later replication through two rounds of replication. These RT changes were confirmed in individual cells by single-cell DNA replication sequencing. Coordinate changes between a shift toward earlier replication and transcriptional activation of adipogenesis-associated genes were observed. RT changes occur before full expression of these genes, indicating that RT reorganization may contribute to the mature adipocyte phenotype. To support this, cells undergoing two rounds of DNA replication during MCE have higher potential to differentiate into lipid droplet-accumulating adipocytes, compared with cells undergoing a single round of DNA replication and non-replicating cells.

2022-12-22 | GSE216765 | GEO

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

Project description:Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

| PRJNA895359 | ENA

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

2022-12-22 | GSE216767 | GEO

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-12-22 | GSE216768 | GEO

SIRT6 is Essential for Adipocyte Differentiation through Regulating Mitotic Clonal Expansion

Project description:Preadipocytes initiate differentiation into adipocytes through a cascade of events. Mitotic clonal expansion, as one of the earliest event, is essential for adipogenesis. However, the underlying mechanisms that regulate mitotic clonal expansion remain elusive. SIRT6 is a member of the evolutionarily conserved sirtuin family of NAD+ dependent protein deacetylases and plays roles in genomic stability, aging, glucose metabolism and inflammatory response. Here, we show that SIRT6 deficiency in preadipocytes blocked their adipogenesis. Analysis of gene expression during adipogenesis reveals that KIF5C, which belongs to kinesin family, is negatively regulated by SIRT6. Furthermore, we show that KIF5C is a negative factor for adipogenesis through interacting with CK2α’, a catalytic subunit of CK2. This interaction blocks CK2α’ nuclear translocation and CK2 kinase activity, and inhibits mitotic clonal expansion during adipogenesis. Thus, SIRT6 acts as an important factor of adipogenesis through inhibiting KIF5C expression and enhancing CK2 kinase activity.

2018-01-16 | GSE94058 | GEO

FTO influences adipogenesis by regulating mitotic clonal expansion.

Project description:The fat mass and obesity-associated (FTO) gene plays a pivotal role in regulating body weight and fat mass; however, the underlying mechanisms are poorly understood. Here we show that primary adipocytes and mouse embryonic fibroblasts (MEFs) derived from FTO overexpression (FTO-4) mice exhibit increased potential for adipogenic differentiation, while MEFs derived from FTO knockout (FTO-KO) mice show reduced adipogenesis. As predicted from these findings, fat pads from FTO-4 mice fed a high-fat diet show more numerous adipocytes. FTO influences adipogenesis by regulating events early in adipogenesis, during the process of mitotic clonal expansion. The effect of FTO on adipogenesis appears to be mediated via enhanced expression of the pro-adipogenic short isoform of RUNX1T1, which enhanced adipocyte proliferation, and is increased in FTO-4 MEFs and reduced in FTO-KO MEFs. Our findings provide novel mechanistic insight into how upregulation of FTO leads to obesity.

| S-EPMC4410642 | biostudies-literature

RNF20 affects porcine adipocyte differentiation via regulation of mitotic clonal expansion.

Project description:ObjectivesRNF20 is recognized as a main E3 ligase for monoubiquitination of histone H2B at lysine 120 (H2Bub). The critical role of RNF20 and H2Bub in various molecular events, such as DNA replication, RNA transcription, and DNA damage response, has been widely investigated and documented. However, its role in porcine adipogenesis remains unknown. In this study, we aimed to clarify the effect of RNF20 on porcine preadipocyte differentiation.Materials and methodsBackfat tissues from fat-type pigs (Bama and Meishan) and lean-type pigs (Yorkshire and Landrace) were collected to detect the expression level of RNF20. Preadipocytes were isolated from Bama piglets and induced to differentiation. Small interfering RNAs were applied to deplete RNF20. Oil Red O staining, quantitative real-time PCR, RNA-seq, Western blot analysis, and EdU assays were performed to study the regulatory mechanism of RNF20 during adipogenesis.ResultsWe found that the expression levels of RNF20 and H2Bub were significantly higher in backfat tissues from fat-type pigs than in those from lean-type pigs. Consistently, the significantly induced expression of RNF20 and H2Bub was also observed in porcine differentiated adipocytes. In addition, knockdown of RNF20 greatly inhibited porcine adipogenesis, as evidenced by dramatically decreased lipid droplet formation and lower expression levels of adipogenic transcription masters in RNF20 knockdown cells. Mechanistically, the depletion of RNF20 decreases the cell proliferation and the level of p-C/EBPβ via the Ras-Raf-MEK1/2-ERK1/2 cascade pathway at the mitotic clonal expansion phase and therefore suppresses cell differentiation.ConclusionsOur results demonstrate that RNF20 is required for porcine preadipocyte differentiation.

| S-EPMC8666272 | biostudies-literature

SIRT6 Is Essential for Adipocyte Differentiation by Regulating Mitotic Clonal Expansion.

Project description:Preadipocytes initiate differentiation into adipocytes through a cascade of events. Mitotic clonal expansion, as one of the earliest events, is essential for adipogenesis. However, the underlying mechanisms that regulate mitotic clonal expansion remain elusive. SIRT6 is a member of the evolutionarily conserved sirtuin family of nicotinamide adenine dinucleotide (NAD)+-dependent protein deacetylases. Here, we show that SIRT6 deficiency in preadipocytes blocks their adipogenesis. Analysis of gene expression during adipogenesis reveals that KIF5C, which belongs to the kinesin family, is negatively regulated by SIRT6. Furthermore, we show that KIF5C is a negative factor for adipogenesis through interacting with CK2α', a catalytic subunit of CK2. This interaction blocks CK2α' nuclear translocation and CK2 kinase activity and inhibits mitotic clonal expansion during adipogenesis. These findings reveal a crucial role of SIRT6 in adipogenesis and provide potential therapeutic targets for obesity.

| S-EPMC9396928 | biostudies-literature

GDE5 inhibition accumulates intracellular glycerophosphocholine and suppresses adipogenesis at a mitotic clonal expansion stage.

Project description:Mammalian glycerophosphodiesterases (GDEs) were recently shown to be involved in multiple cellular signaling pathways. This study showed that decreased GDE5 expression results in accumulation of intracellular glycerophosphocholine (GPC), showing that GDE5 is actively involved in GPC/choline metabolism in 3T3-L1 adipocytes. Using 3T3-L1 adipocytes, we further studied the biological significance of GPC/choline metabolism during adipocyte differentiation. Inhibition of GDE5 suppressed the formation of lipid droplets, which is accompanied by the decreased expression of adipocyte differentiation markers. We further showed that the decreased GDE5 expression suppressed mitotic clonal expansion (MCE) of preadipocytes. Decreased expression of CTP: phosphocholine cytidylyltransferase (CCT?), a rate-limiting enzyme for phosphatidylcholine (PC) synthesis, is similarly able to inhibit MCE and PC synthesis; however, the decreased GDE5 expression resulted in accumulation of intracellular GPC but did not affect PC synthesis. Furthermore, we showed that mRNAs of proteoglycans and transporters for organic osmolytes are significantly upregulated and that intracellular amino acids and urea levels are altered in response to GDE5 inhibition. Finally, we showed that reduction of GDE5 expression increased lactate dehydrogenase release from preadipocytes. These observations indicate that decreased GDE5 expression can suppress adipocyte differentiation not through the PC pathway but possibly by intracellular GPC accumulation. These results provide insight into the roles of mammalian GDEs and their dependence upon osmotic regulation by altering intracellular GPC levels.

| S-EPMC6397339 | biostudies-literature

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