Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Joanna DiSpirito
PROVIDER: E-GEOD-48345 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:"Master" transcription factors are the gatekeepers of lineage identity. As such, they have been a major focus of efforts to manipulate cell fate for therapeutic purposes. The ETS transcription factor PU.1 has a potent ability to confer macrophage phenotypes on cells already committed to a different lineage, but how it overcomes the presence of other master regulators is not known. The nuclear receptor PPARM-NM-3 is the master regulator of the adipose lineage, and its genomic binding pattern is well characterized in adipocytes. Here, we show that when expressed at macrophage levels in mature adipocytes, PU.1 bound a large fraction of its macrophage sites, where it induced chromatin opening and the expression of macrophage target genes. Strikingly, PU.1 markedly reduced the genomic binding of PPARM-NM-3 without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARM-NM-3 binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARM-NM-3 cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator. ChIP-seq was performed on 3T3-L1 adipocytes from two treatment groups: (1) adipocytes transduced with a control adenovirus expressing beta-galactosidase (LACZ-Ads) and (2) adipocytes transduced with an adenovirus expressing full-length murine PU.1 cDNA (PU.1-Ads). Nuclear lysates from each group were used for PPARg ChIP. For PU.1-Ads, PU.1 ChIP was also performed. To generate chromatin for ChIP-seq, DNA from three immunoprecipitations per condition was pooled. This process was repreated from a second set of L1 adipocytes to generate two biological replicates for sequencing. Genomic input DNA was sequenced from the first biological replicate only.
2013-06-27 | E-GEOD-48343 | biostudies-arrayexpress
Project description:Master transcription factors are the gatekeepers of lineage identity. As such, they have been a major focus of efforts to manipulate cell fate for therapeutic purposes. The ETS transcription factor PU.1 has a potent ability to confer macrophage phenotypes on cells already committed to a different lineage, but how it overcomes the presence of other master regulators is not known. The nuclear receptor PPARγ is the master regulator of the adipose lineage, and its genomic binding pattern is well characterized in adipocytes. Here, we show that when expressed at macrophage levels in mature adipocytes, PU.1 bound a large fraction of its macrophage sites, where it induced chromatin opening and the expression of macrophage target genes. Strikingly, PU.1 markedly reduced the genomic binding of PPARγ without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARγ binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARγ cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator. Microarray expression profiling was performed on 3T3-L1 adipocytes from two treatment groups: (1) adipocytes transduced with a control adenovirus expressing beta-galactosidase (LACZ-Ads) and (2) adipocytes transduced with an adenovirus expressing full-length murine PU.1 cDNA (PU.1-Ads). Each sample group consists of four biological replicates which are here defined as separate differentiations of mature 3T3-L1 adipocytes and adenoviral infections. Each replicate was hybridized to an individual array for a total of eight arrays.
2013-06-27 | E-GEOD-48344 | biostudies-arrayexpress
Project description:We use ChIP-seq to discover the genome-wide sites of acetylation of lysine 56 of the histone H3 (H3K56), which is a target of three histone modifying enzymes with known roles in diabetes and insulin resistance, in human adipocytes derived from mesenchymal stem cells. Surprisingly, we find that a very large fraction of genes show some level of acetylation on H3K56, but the highest levels of acetylation are associated with genes previously reported to be involved in type 2 diabetes. Using computational methods, we propose that the transcription factor E2F4 may be involved in recruiting histone modifying enzymes to these sites. We confirm this prediction by measuring the binding of E2F4 using ChIP-seq. We also examine the binding of two other proteins using ChIP-Seq: HSF-1 and C/EBPM-NM-1M-BM- . HSF-1 is a master regulator of stress responses, and is a target of the same histone modifiers as H3K56. We find a high degree of overlap between HSF-1 binding and H3K56 acetylation even in cells that are not stressed. By contrast, C/EBPM-NM-1M-BM- , which is not known to be modified by these enzymes, shows much less overlap with the sites of H3K56 acetylation. Our results represent the first mapping of the regulatory code of human adipocytes. Examination of H3K56 acetylation sites and E2F4,C/EBPM-NM-1 and HSF-1 binding sites in human adipocytes.
2011-05-31 | E-GEOD-24326 | biostudies-arrayexpress
Project description:The winged helix protein FOXA2 and the nuclear receptor PPARg are highly conserved, regionally-expressed transcription factors that regulate networks of genes controlling complex metabolic functions. Cistrome analysis for FOXA2 in mouse liver and PPARg in mouse adipocytes has previously produced consensus binding sites that are nearly identical to those used by the factors in human cells. Despite this conservation of the canonical binding motif, we report here that the great majority of specific binding regions for FOXA2 in human liver and for PPARg in human adipocytes are not in the orthologous locations to the mouse genome. Nevertheless, gene-centric analysis reveals strong shared transcription factor occupancy near genes in tissue-specific metabolic pathways that are functionally conserved across species. Genes with only species-specific binding sites fail to show enrichment for these pathways. Thus, the biological functions of transcription factors that control specific metabolic functions are highly shared across species. Two TFs, FOXA2 and PPARg, were studied for genome-wide conservation of binding between mouse and human in specific tissues/cell-types (liver for FOXA2, adipocytes for PPARg). The number of replicates for each TF was chosen to obtain a comparable number of reads between the TFs and species. Human FOXA2 ChIP-seq was performed on two biological replicates of human liver samples, in three technical replicates each. Input DNA was also collected and sequenced from both biological samples. Mouse FOXA2 ChIP-seq was performed on four biological replicates of mouse liver samples. The ChIP and sequencing were repeated on two of these biological replicates to create technical replicates for additional sequence reads. Input DNA was sequenced from three additional mouse livers. Human PPARg ChIP-seq was performed on a human adipocyte cell-line (SGBS) differentiated in two replicate cultures. Input DNA was also collected and sequenced from one culture. Mouse PPARg ChIP-seq was performed on 3T3-L1 cells differentiated into adipocytes in culture in a single replicate, and this sequence data was pooled with existing data previously generated by the same lab, already available in GEO (GSE21314). A standard pool of input DNA sample sequence from multiple mouse tissue was used for analyzing the Mouse PPARg ChIP-seq data.
2011-04-06 | E-GEOD-25836 | biostudies-arrayexpress
Project description:Plasmodium falciparum gametocyte stages represent a small fraction of the entire parasite biomass that is present during human malaria infection, yet they alone lead to the transmission of this devastating disease. One of the critical gaps in malaria transmission biology and surveillance is our lack of knowledge about gametocyte biology, especially sexual dimorphic development that may influence transmission from the human to the mosquito. Ratios of male and female gametocytes in the peripheral blood can vary significantly; influenced in part by asexual blood stage and gametocyte density as well as vertebrate and invertebrate host factors. Moreover, the role of sex ratios on gametocyte transmission potential to mosquitoes is unknown and dissecting this process has been hampered by the lack of sex-specific protein markers for the circulating, mature stage V gametocytes. The current evidence suggests a high degree of conservation in gametocyte gene complement across Plasmodium, and therefore presumably for sex-specific genes as well. Therefore, to better our understanding of gametocyte development and subsequent infectiousness to mosquitoes, we undertook a two pronged approach. First, we acquired the mixed, male and female stage V gametocyte proteomes of the NF54 isolate and mature stage V female proteome from Dd2, a strain that is defective in producing mature males. Second, we then undertook a Systematic Subtractive Bioinformatic analysis (filtering) approach to identify sex-specific P. falciparum NF54 protein markers based on a comparison with the Dd2 strain and syntenic male and female proteins from the reanalyzed and updated P. berghei (related rodent malaria parasite) gametocyte proteomes. This has produced a short list of putative 174 male- and 258 female-specific P. falciparum stage V proteins. Furthermore, we generated antibodies against three putative female-specific gametocyte stage V proteins in P. falciparum and confirmed sex-specificity for two proteins and also the loss sex-partitioning for a putative female-specific protein in rodent malaria parasites.
2014-07-25 | PXD000813 | Pride
Project description:There are an estimated 21million diabetics in the United States and 150 million diabetics worldwide. The World Health Organization anticipates that these numbers will double in the next 20 years. Metabolic syndrome is a well recognized set of symptoms that increases a patient’s risk of developing diabetes. Insulin resistance is a factor in both metabolic syndrome and Type 2 diabetes. It is characterized by decreased insulin stimulated glucose uptake in peripheral tissues, decreased adiponectin levels, increased adipocyte FFA and cytokine production, and increased insulin and hepatic glucose output. Prevention or reversal of insulin resistance should serve as an important strategy in addressing the growing health concerns posed by the Diabetes epidemic. While increased adiposity is associated with insulin resistance, the role of the cell types present within adipose (adipocytes, pre-adipocytes, endothelial cells, macrophages, fibroblasts, leukocytes and smooth muscle cells) in insulin resistance is unclear. In an effort to begin dissection of this question, we examined the transcriptional response of the buoyant and non-buoyant fractions isolated from insulin sensitive or TNF induced insulin resistant hMSC derived adipocytes before and after treatment with insulin. hMSC derived adipocytes were treated with 0 or 10ng/ml TNF for 24 hours to induce insulin resistance and subsequently serum starved for 5 h followed by treatment with 0 or 20nM insulin for 2 hours. At the end of the incubation period, cells were harvested as is (mixed) or subjected to fractionation to separate the adipocytes (buoyant fraction) and the stromal cells (non-buoyant fraction). These isolated cells were resuspended in RLT buffer to prepare lysates for total RNA isolation using the Qiagen RNeasy kit. Total RNA was submitted to GeneLogic for cRNA preparation using the Affymetrix GenChip IVT kit and hybridization to Affymetrix U133 Plus 2.0 arrays.
2010-11-30 | E-GEOD-24422 | biostudies-arrayexpress
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2013-11-19 | E-GEOD-41578 | biostudies-arrayexpress
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