Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE216767 | GEO | 2022/12/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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

Integrative genomics reveal a role for MCPIP1 in adipogenesis and adipocyte metabolism

Project description:Obesity is considered a serious chronic disease, which is associated with increased risk of developing cardiovascular diseases, non-alcoholic fatty liver disease and type 2 diabetes. Monocyte chemoattractant protein-1-induced protein-1 (MCPIP1), also called Regnase-1, is an RNase that decreases stability of transcripts coding for inflammation-related proteins. In addition, MCPIP1 plays an important role in the regulation of adipogenesis in vitro by reducing the expression of key transcription factors, including C/EBPβ and PPARγ, during adipocyte differentiation. Here we present RNA-Seq and proteomic analysis of 3T3-L1 adipocytes overexpressing wild-type MCPIP1 (WTMCPIP1) and mutant MCPIP1 (D141NMCPIP1) at day 2 and 4 of differentiation, respectively. RNA-Seq analysis followed by confirmatory Q-RT-PCR revealed that elevated MCPIP1 levels in 3T3-L1 adipocytes upregulated transcripts encoding proteins involved in signal transmission and cellular remodeling and downregulated transcripts of factors involved in metabolism. These data are consistent with our LC-MS/MS analysis, which showed that MCPIP1 expressing adipocytes exhibit upregulation of proteins involved in cellular organization and movement and decreased levels of proteins involved in lipid and carbohydrate metabolism. Moreover, MCPIP1 adipocytes are characterized by decreased Glut4 levels and impaired glucose uptake. Overall, our ﬁndings demonstrate that MCPIP1 is an important regulator of adipogenesis and adipocyte metabolism.

2020-01-07 | PXD010148 | Pride

Gene expression signatures in 3T3-L1 adipocytes 2, 8 and 20 days after the induction of adipocyte differentiation

Project description:To identify the genes that increase in hypertrophic adipocytes, we have performed DNA microarray analysis in 3T3-L1 adipocytes. Hypertrophic adipocytes were obtained by long-term culture in routine cell culture medium. 2, 8 and 20 days after the induction of adipogenesis, total RNA was isolated.

2020-04-01 | GSE147858 | GEO

Gene expression signatures in IRF7 overexpressed 3T3-L1 adipocytes

Project description:To identify the genes that are regulated by IRF7, we have performed DNA microarray in 3T3-L1 adipocytes differentiated from precursor cells infected with retrovirus empty or carrying IRF7. Plasmids (Empty- and IRF7-pMSCV) were kindly provided from Dr. Eguchi at the Okayama University Graduate School of Medicine, Okayama, Japan [Cell Metab. 2008;7: 86-94.]. Infected 3T3-L1 preadipocytes were selected by puromycin treatment and differentiated into adipocytes. 7 days after the induction of adipogenesis, total RNA was isolated.

2020-04-01 | GSE147857 | GEO

YG001: A Usp7-Tip60 pathway regulates early adipogenesis

Project description:USP7, a dominant DUB activity in 3T3-L1 adipocytes and in mouse adipose tissue, increases Tip60 protein levels, and deubiquitinates Tip60 both in intact cells and in vitro. Treatment with a pan deubiquitinase (DUB) inhibitor, or knockdown of USP7, decreases adipogenesis. Transcriptome analysis reveals a common set of cell cycle genes to be co-regulated by both Tip60 and USP7. Knock down of either factor results in impaired mitotic clonal expansion, an early step in adipogenesis. These results therefore reveal deubiquitination of a transcriptional coregulator to be a key mechanism in the regulation of early adipogenesis Mature 3T3-L1 adipocytes were subjected to RNAi-mediated knock down with control(C), USP7(U)- or Tip60(T)-specific oligonucleotides. For this, 4 replicates of differentiated 3T3-L1 cells were transfected with Amaxa technology. Two days after transfection cells were washed twice with PBS twice and lysed in 0.5ml Trizol (Invitrogen). mRNA expression of Tip60 and USP7 was assessed by qRT-PCR. Amplified cRNA samples were labeled with either cy3 or cy5 and put on microarray together with and oppositely labeled common reference sample consisting of cRNA derived from undifferentiated 3T3-L1 cells.

2013-08-28 | E-GEOD-28587 | biostudies-arrayexpress

The effects of silencing PCYOX1 on the proteome of murine fibroblast cells 3t3-L1 differentiated to adipocyte-like cells

Project description:In order to evaluate the impact of PCYOX1 deletion on adipogenesis, we applied a label-free mass spectrometry-based proteomic approach to compare the proteome of 3T3-L1 differentiated for 9 days to adipocytes after PCYOX1 gene silencing. Pcyox1 was silenced using shRNA lentiviral particles. Control cells were treated with shRNA lentiviral particles containing a negative construct.

2023-05-10 | PXD039943 | Pride

Detection of microRNA expression during 3T3-L1 pre-adipocyte differentiation using a custom made microarray chip.

Project description:Differentiation of 3T3-L1 cells into adipocytes involves a highly orchestrated series of events including clonal expansion, growth arrest and terminal differentiation. The mechanisms coordinating these different steps are not yet fully understood. Here we investigated whether micro (mi)RNAs play a role in this process. Microarray analysis was performed to detect miRNA expression during 3T3-L1 preadipocyte differentiation. Several miRNAs, including let-7, were up-regulated during 3T3-L1 adipogenesis. Ectopic introduction of let-7 into 3T3-L1 cells inhibited clonal expansion as well as terminal differentiation. The mRNA encoding high mobility group AT-hook 2 (HMGA2), a transcription factor that regulates growth and proliferation in other contexts, was inversely correlated with let-7 levels during 3T3-L1 cell adipogenesis, and let-7 markedly reduced HMGA2 concentrations. Knockdown of HMGA2 inhibited 3T3-L1 differentiation. These results suggest that let-7 plays an important role in adipocyte differentiation and that it does so in part by targeting HMGA2, thereby regulating the transition from clonal expansion to terminal differentiation. 3T3-L1 cells were induced to differentiation into mature adipocytes using a canonical DMI cocktail. The time point at two days after confluency of 3T3-L1 was defined as day 0. Samples were collected at day 0, day 1, day 4, and day 7. The expression of microRNAs at day 1, day 4, and day 7 was compared to that of day 0.

2010-05-18 | E-GEOD-16229 | biostudies-arrayexpress

Early adipogenesis is repressed through the newly identified FHL2-NFAT5 signaling complex

Project description:The LIM-domain-only protein FHL2 is a modulator of signal transduction and has been shown to direct the differentiation of mesenchymal stem cells toward osteoblasts and myocytes phenotypes. We hypothesized that FHL2 may simultaneously interfere with the induction of the adipocyte lineage. Therefore, we investigated the role of FHL2 in adipocyte differentiation using pre-adipocytes isolated from mouse adipose tissue and the 3T3-L1 (pre)adipocyte cell line. Here we report that FHL2 is expressed in pre-adipocytes and for accurate adipocyte differentiation, this protein needs to be downregulated during the early stages of adipogenesis. More specifically, constitutive overexpression of FHL2 drastically inhibits adipocyte differentiation in 3T3-L1 cells, which was demonstrated by suppressed activation of the adipogenic gene expression program as shown by extensive RNAseq analyses, and diminished lipid accumulation. To identify the protein-protein interactions mediating this repressive activity of FHL2 on adipogenesis, we performed affinity-purification mass spectrometry (AP-MS). This analysis revealed the interaction of FHL2 with the Nuclear factor of activated T-cells 5 (NFAT5), an established inhibitor of adipocyte differentiation. NFAT5 knockdown rescued the inhibitory effect of FHL2 overexpression on 3T3-L1 differentiation, indicating that these proteins act cooperatively. In conclusion, we present a new regulatory function of FHL2 in early adipocyte differentiation and revealed that FHL2-mediated inhibition of pre-adipocyte differentiation is dependent on its interaction with NFAT5.

2023-11-13 | PXD033974 | Pride

iTRAQ-Based Quantitative Proteomic Comparison of 2D and 3D Adipocyte Cell Models Co-cultured with Macrophages Using Online 2D-nanoLC-ESI-MS/MS

Project description:The demand for novel three-dimensional (3D) cell culture models of adipose tissue has been increasing, and proteomic investigations are important for determining the underlying causes of obesity, type II diabetes, and metabolic disorders. In this study, we performed global quantitative proteomic profiling of three 3D-cultured 3T3-L1 cells (preadipocytes, adipocytes and co-cultured adipocytes with macrophages) and their 2D-cultured counterparts using 2D-nanoLC-ESI-MS/MS with iTRAQ labelling. A total of 2,885 shared proteins from six types of adipose cells were identified and quantified in four replicates. Using iTRAQ-based quantitative assessments, we found that the primary proteins involved in carbohydrate and fatty acid metabolism, adipogenesis and the electron transport chain were highly expressed in 3D cell culture system when compared to those of 2D-cultured cells. Furthermore, it was also shown that the expression levels of proteins associated with metabolic pathways, carbon metabolism and glycolysis/gluconeogenesis were up-regulated, whereas proteins implicated in both DNA replication and the cell cycle were expressed at lower levels compared to those of the 2D mono-cultured cells. Based on these results, the 3D adipocyte model can help elucidate the mechanisms underpinning metabolic syndromes and aid the development of new medical treatments for metabolic disorders.

2020-05-26 | PXD014437 | Pride

Resveratrol treatment of 3T3-L1 cells

Project description:Murine 3T3-L1 progenitor adipocytes cell cultures, treated and untreated (Control) with resveratrol before the induction of differentiation and the effects on adipogenesis and insulin signaling was investigated. Keywords: Treatment response

2012-12-25 | GSE7111 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data