Comprehensive analysis of mRNA and lncRNA transcriptomes reveals the differentially hypoxic response of preadipocytes during adipogenesis
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ABSTRACT:
PROVIDER: PRJNA601957 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10908300.fastq.gz | Fastqsanger.gz | |||
| SRR10908301.fastq.gz | Fastqsanger.gz | |||
| SRR10908302.fastq.gz | Fastqsanger.gz | |||
| SRR10908303.fastq.gz | Fastqsanger.gz | |||
| SRR10908304.fastq.gz | Fastqsanger.gz |
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Project description:Local hypoxia is recently reported to be occur in white adipose tissue (WAT) microenvironment at obesity. Adipocyte have own life cycle that reflect in different stages of adipogenesis in WAT niche. Long noncoding RNAs (lncRNAs) play an important role in cellular response to hypoxia. However, the different hypoxic responses of preadipocytes during adipogenesis and the potential role of lncRNAs in this process remain to be elucidated. Here we evaluated the different hypoxic responses of primary hamster preadipocytes during adipogenesis and analyzed the expression of mRNAs and lncRNAs from same Ribo-Zero RNA-seq libraries. Hypoxia induced HIF-1α protein during adipogenesis and caused the divergent changes of cell phenotypes. A total of 10,318 mRNAs were identified to be expressed in twenty libraries (five timepoints), and 149, 326, 365, 1099, 2504 differentially expressed mRNAs (DE mRNAs) were detected in D0, D1, D3, D7 and D11, respectively (hypoxia vs normoxia). Functional enrichment analysis revealed the shared and specific hypoxia response pathways in different stages of adipogenesis. Hypoxia differentially modulates the expression profile of adipose-associated genes, including adipokines, lipogenesis, lipolysis, hyperplasia, hypertrophy, inflammatory and extracellular matrix (ECM). We also identified 4,296 lncRNAs that were substantially expressed and detected 1,431 DE lncRNAs in five timepoints. Afterward, 2, 3, 5, 13 and 50 DE mRNAs in D0, D1, D3, D7 and D11, respectively, were highly correlated and loci-nearby with DE lncRNAs, and were mainly involved in cell cycle, vesicle-mediated transport and mitochondrion organization. We also identified twenty-eight one-to-one lncRNA-mRNA pairs that might be closely related to adipocyte function, such as ENSCGRT00015041780-Hilpda, TU2105-Cdsn, TU17588-Ltbp3. These lncRNAs may represent the crucial regulation axis in cellular response to hypoxia during adipogenesis. Altogether, this study dissected the effects of hypoxia in the cell during adipogenesis, and uncovered novel regulator potentially associated with obesity and may provide a new view for interpretation and treatment of obesity.
2020-01-18 | GSE143873 | GEO
Project description:Local hypoxia has recently been reported to occur in the white adipose tissue (WAT) microenvironment during obesity. Adipocytes have a unique life cycle that reflects the different stages of adipogenesis in the WAT niche. Long non-coding RNAs (lncRNAs) play an important role in the cellular response to hypoxia. However, the differentially hypoxic responses of preadipocytes during adipogenesis and the potential role of lncRNAs in this process remain to be elucidated. Here, we evaluated the differentially hypoxic responses of primary hamster preadipocytes during adipogenesis and analyzed mRNA and lncRNA expression in same Ribo-Zero RNA-seq libraries. Hypoxia induced HIF-1α protein during adipogenesis and caused divergent changes of cell phenotypes. A total of 10,318 mRNAs were identified to be expressed in twenty libraries (five timepoints), and 3,198 differentially expressed mRNAs (DE mRNAs) were detected at five timepoints (hypoxia vs. normoxia). Functional enrichment analysis revealed the shared and specific hypoxia response pathways in the different stages of adipogenesis. Hypoxia differentially modulated the expression profile of adipose-associated genes, including adipokines, lipogenesis, lipolysis, hyperplasia, hypertrophy, inflammatory, and extracellular matrix. We also identified 4,296 lncRNAs that were expressed substantially and detected 1,431 DE lncRNAs at five timepoints. Two, 3, 5, 13, and 50 DE mRNAs at D0, D1, D3, D7, and D11, respectively, were highly correlated and locus-nearby DE lncRNAs and mainly involved in the cell cycle, vesicle-mediated transport, and mitochondrion organization. We identified 28 one-to-one lncRNA-mRNA pairs that might be closely related to adipocyte functions, such as ENSCGRT00015041780-Hilpda, TU2105-Cdsn, and TU17588-Ltbp3. These lncRNAs may represent the crucial regulation axis in the cellular response to hypoxia during adipogenesis. This study dissected the effects of hypoxia in the cell during adipogenesis, uncovered novel regulators potentially associated with WAT function, and may provide a new viewpoint for interpretation and treatment of obesity.
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2010-03-19 | E-GEOD-20054 | biostudies-arrayexpress
Project description:Dexamethasone (DEX), a synthetic ligand for glucocorticoid receptor (GR), is routinely used to stimulate adipogenesis in culture. GR-depleted preadipocytes show adipogenesis defects one week after induction of differentiation. However, it has remained unclear whether GR is required for adipogenesis in vivo. By deleting GR in precursors of brown adipocytes, we found unexpectedly that GR is dispensable for brown adipose tissue development in mice. In culture, GR-deficient primary or immortalized white and brown preadipocytes showed severely delayed adipogenesis one week after induction of differentiation. However, when differentiation was extended to 3 weeks, GR-deficient preadipocytes showed similar levels of adipogenesis marker expression and lipid accumulation as the wild type cells, indicating that DEX-bound GR accelerates, but is dispensable for, adipogenesis. Consistently, DEX accelerates, but is dispensable for, adipogenesis in culture. We show that DEX-bound GR accelerates adipogenesis by directly promoting the expression of adipogenic transcription factors C/EBPb, C/EBPd, C/EBPa, KLF5, KLF9 and PPARg in the early phase of differentiation. Mechanistically, DEX-bound GR recruits histone H3K27 acetyltransferase CBP to promote activation of C/EBPb-primed enhancers of adipogenic genes. These results clarify the role of GR in adipogenesis in vivo and demonstrate that DEX-mediated activation of GR accelerates, but is dispensable for, adipogenesis.
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