Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor γ Function in Adipocytes and Macrophages

Abstract

The nuclear receptor peroxisome proliferator activator receptor ␥ (PPAR␥) is the target of antidiabetic thiazolidinedione drugs, which improve insulin resistance but have side effects that limit widespread use. PPAR␥ is required for adipocyte differentiation, but it is also expressed in other cell types, notably macrophages, where it influences atherosclerosis, insulin resistance, and inflammation. A central question is whether PPAR␥ binding in macrophages occurs at genomic locations the same as or different from those in adipocytes. Here, utilizing chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), we demonstrate that PPAR␥ cistromes in mouse adipocytes and macrophages are predominantly cell type specific. In thioglycolate-elicited macrophages, PPAR␥ colocalizes with the hematopoietic transcription factor PU.1 in areas of open chromatin and histone acetylation, near a distinct set of immune genes in addition to a number of metabolic genes shared with adipocytes. In adipocytes, the macrophage-unique binding regions are marked with repressive histone modifications, typically associated with local chromatin compaction and gene silencing. PPAR␥, when introduced into preadipocytes, bound only to regions depleted of repressive histone modifications, where it increased DNA accessibility, enhanced histone acetylation, and induced gene expression. Thus, the cell specificity of PPAR␥ function is regulated by cell-specific transcription factors, chromatin accessibility, and histone marks. Our data support the existence of an epigenomic hierarchy in which PPAR␥ binding to cell-specific sites not marked by repressive marks opens chromatin and leads to local activation marks, including histone acetylation.Peroxisome proliferator-activated receptor ␥ (PPAR␥) is a nuclear receptor that regulates essential aspects of adipocyte biology, including insulin sensitivity, lipogenesis, and survival, and is the target of anti-diabetic thiazolidinedione drugs (39, 69). Recent genome-wide studies of adipocytes (40,53) have demonstrated that PPAR␥ localizes preferentially to lipid and carbohydrate metabolism genes, many of which are downregulated by PPAR␥ knockdown (62). It has also become apparent that in vivo PPAR␥ binding occurs predominantly as a heterodimer with retinoid X receptor (RXR) at direct repeats of the sequence AGGTCA separated by a single base pair, i.e., DR1 elements, as predicted by in vitro studies and a small number of previously known target genes (61). Furthermore, CCAAT/enhancer-binding proteins (C/EBPs) were found to colocalize with PPAR␥ at the majority of its binding sites and to have cooperative effects on target gene transcription (40).The two isoforms of PPAR␥, ␥1 and ␥2, are transcribed from alternative start sites and are most abundant in adipocytes, which require PPAR␥ for differentiation (39, 69), although other cell types express lower levels of the ␥1 isoform (10, 72). Among these, macrophages have garnered much attention for their ability to affect metabolism in a number of tissues...

LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function

“…Thus, ChIP-seq data alone are insufficient to predict the LRH-1-regulated targets in a tissue. Similar comparisons of mRNA regulation and ChIP-seq for other transcription factors, including estrogen receptor a, peroxisome proliferator-activated receptor g, and RBPJL, have also revealed that only a small fraction of binding sites contributes to gene regulation in the context of a particular tissue (Carroll et al 2006;Nielsen et al 2008;Lefterova et al 2010;Masui et al 2010).…”

Command line analysis of ChIP-seq results

“…Example of the statistics extracted from the log and result files of the analysis using the get _ tag _ statistics-v1 _ 0. sh script. The raw sequence data for the basic analysis with the ChIP-seq _ anal-v1 _ 0.sh script were obtained from different sources [11][12][13][14]. not only for processing our own data but also to compare our data to other's, or simply to make a ChIP-seq meta-analysis using the available ChIP-seq raw sequence data at the sequence read repositories.…”

“…Installing HOMER is very simple, we only need to have the proper Figure 1. Motif finding result using parallel MEME on a macrophage PPARg ChIP result [14].…”

The Role of Prolyl Hydroxylase Domain Protein (PHD) during Rosiglitazone-induced Adipocyte Differentiation

“…Furthermore, the PPAR␥ antagonists BADGE and GW1882 abolished rosiglitazone-induced PHD expression, indicating that PHD induction by rosiglitazone is mediated by PPAR␥. Previous reports suggest that there are potential PPAR␥ binding sites in the promoter region of PHDs on the basis of the PPAR␥ ChIP sequence database in 3T3-L1 adipocytes (27,28). FIGURE 9.…”