Genome-wide binding sites of HOXC4 in brown adipocytes
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ABSTRACT:
PROVIDER: PRJNA1108324 | ENA |
REPOSITORIES: ENA
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Project description:We found that overexpression of HOXC4 in mature adipocytes enhances thermogenesis. To investigate the binding sites of HOXC4 in the genome of brown adipocytes, we performed HOXC4 ChIP-seq experiments on differentiated primary brown adipocytes, which overexpressed HOXC4.
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Project description:Aberrant expression of HOXC6 and HOXC4 is commonly detected in prostate cancer. The high expression of these transcription factors is associated with aggressive prostate cancer and can predict cancer recurrence after treatment. Thus, HOXC4 and HOXC6 are clinically relevant biomarkers of aggressive prostate cancer. However, the molecular mechanisms by which these HOXC genes contribute to prostate cancer is not yet understood. To begin to address the role of HOXC4 and HOXC6 in prostate cancer, we performed RNA-seq analyses before and after siRNA-mediated knockdown of HOXC4 and/or HOXC6 and also performed ChIP-seq to identify genomic binding sites for both of these transcription factors. Our studies demonstrate that HOXC4 and HOXC6 co-localize with HOXB13, FOXA1 and AR, three transcription factors previously shown to contribute to the development of prostate cancer. We suggest that the aberrantly upregulated HOXC4 and HOXC6 proteins may compete with HOXB13 for binding sites, thus altering the prostate transcriptome. This competition model may be applicable to many different human cancers that display increased expression of a HOX transcription factor.
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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.
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Project description:We have identified a population of adipocytes in fat tissue that arise from bone marrow-derived progenitor cells. We used microarrays to compare the global gene expression patterns of the bone marrow progenitor-derived adipocytes as well as conventional white and brown adipocytes to evaluate the relationship between these adipocyte subpopulations.
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Project description:Cre recombinase activity was induced in differentiating brown adipocytes from CreERT2 Sykflox/flox mice in vitro, which resulted in a partial loss of Syk protein in mature brown adipocytes. Such cells were viable, morphologically normal and displayed largely normal gene expression as indicated by mRNA sequencing and qPCR analysis, suggesting that Syk is not required for survival and gene expression of terminally differentiated brown adipocytes. mRNA sequencing of Syk depleted brown adipocytes treated with 0.1 microM isoproterenol for 6 h showed that 2460 genes were not induced or suppressed upon stimulation. Gene set enrichment analysis revealed a great enrichment for genes essential for mitochondrial respiration and biogenesis, for genes associated with and required for adipogenesis, as well as for genes responsive to various stimuli in adipocytes among genes highly ranked by reduced fold changes in response to isoproterenol in the Syk deficient brown adipocytes.
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