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Gene expression and ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE120361 | GEO | 2018/11/08

REPOSITORIES: GEO

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H3K36me3 ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

Project description:During the aging process, bone marrow mesenchymal stem cells (BMSCs) exhibit declined osteogenesis accompanied by excess adipogenesis, which will lead to osteoporosis. Here we report that the H3K36 trimethylation, catalyzed by histone methyltransferase SETD2 regulates lineage commitment of BMSCs. Deletion of Setd2 in mBMSCs, through conditional Cre expression driven by Prx1 promoter, resulted in bone loss and marrow adiposity. Loss of Setd2 in BMSCs in vitro facilitated differentiation propensity to adipocytes rather than to osteoblasts. Through conjoint analysis of RNA-seq and ChIP-seq data, we identified a SETD2 functional target gene, Lbp, on which H3K36me3 was enriched, and its expression was affected by Setd2 deficiency. Furthermore, overexpression of LBP could partially rescue the lack of osteogenesis and enhanced adipogenesis resulted from the absence of Setd2 in BMSCs. Further mechanism study demonstrated that the trimethylation level of H3K36 could regulate Lbp transcriptional initiation and elongation. These findings suggest that H3K36 trimethylation mediated by SETD2 could regulate the cell fate of mesenchymal stem cells in vitro and in vivo, indicating that the regulation of H3K36me3 level by targeting SETD2 and/or the administration of downstream LBP protein may represent potential therapeutic way for new treatment in metabolic bone diseases, such as osteoporosis.

2018-11-08 | GSE120351 | GEO

Gene expression profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre respectively

2018-11-08 | GSE120244 | GEO

H3K36me3 ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

Project description:H3K36me3 ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

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Gene expression and ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

Project description:Gene expression and ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

| PRJNA492881 | ENA

Gene expression profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre respectively

Project description:Gene expression profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre respectively

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LM2 cell: infected with lentivirus to stably express Elf5 vs GFP

Project description:Elf5 induced transcriptional changes in high lung metastasis subline LM2 (MDA-MB-231 origin), control (GFP) vs ELF5 Two-condition experiment, control (GFP) vs Elf5. Each has duplicate biological repeats.

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Gene expression of primary chondrocytes obtained from Hif1afl/fl mice transduced with adenovirus expressing GFP or Cre

Project description:To identify gene expression profiles when Hif1a is deleted in chondrocytes

2020-03-17 | GSE106965 | GEO

LM2 cell: infected with lentivirus to stably express Elf5 vs GFP

Project description:Elf5 induced transcriptional changes in high lung metastasis subline LM2 (MDA-MB-231 origin), control (GFP) vs ELF5

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RNA-Seq analysis of obese Pdha1<sup>fl/fl</sup>Lyz2-Cre mice induced by a high-fat diet.

Project description:Pyruvate dehydrogenase complex (PDH) is an important complex of three enzymes that transforms pyruvate into acetyl-CoA, subsequently entering the tricarboxylic acid (TCA) cycle to produce ATP and electron donors. As a key regulator of energy and metabolic homeostasis, PDH is considered a potential therapeutic target of many diseases. On the other hand, the relationship between PDH and obesity is not clear. In this study, peripheral blood of Pdha1fl/flLyz2-Cre and C57BL/6 mice fed a high-fat diet (HFD) was collected and subjected to extensive transcriptome sequencing. Differentially expressed genes (DEGs) were identified. Enrichment of functions and signaling pathways analyses were performed based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the genes selected from RNA sequencing (RNA-seq). Eventually, we found that Pdha1fl/flLyz2-Cre mice were more susceptible to HFD-induced obesity. A total of 302 up-regulated genes and 30 down-regulated genes were screened that were differentially expressed between Pdha1fl/flLyz2-Cre mice fed the HFD and the control groups. Furthermore, we verified that significant transcriptional changes in the genes Sgstm1, Ncoa4, Rraga, Slc3a2, Usp15, Gabarapl2, Wipi1, Sh3glb1, Mtmr3, and Cd36 were consistent with the results obtained from RNA-seq analysis. In summary, this study preliminarily established that there is a close relationship between Pdha1 and obesity and revealed the possible downstream pathways and target genes involved, laying a good foundation for the further study of Pdha1 function in the future.

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Cell type-specific manipulation with GFP-dependent Cre recombinase.

Project description:There are many transgenic GFP reporter lines that allow the visualization of specific populations of cells. Using such lines for functional studies requires a method that transforms GFP into a molecule that enables genetic manipulation. We developed a method that exploits GFP for gene manipulation, Cre recombinase dependent on GFP (CRE-DOG), a split component system that uses GFP and its derivatives to directly induce Cre/loxP recombination. Using plasmid electroporation and AAV viral vectors, we delivered CRE-DOG to multiple GFP mouse lines, which led to effective recombination selectively in GFP-labeled cells. Furthermore, CRE-DOG enabled optogenetic control of these neurons. Beyond providing a new set of tools for manipulation of gene expression selectively in GFP(+) cells, we found that GFP can be used to reconstitute the activity of a protein not known to have a modular structure, suggesting that this strategy might be applicable to a wide range of proteins.

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