Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis
Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis
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DOI：
10.1101/gad.501108
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发表时间：
2008-11-01
影响因子：
10.5
通讯作者：
Stunnenberg, Hendrik G.
中科院分区：
文献类型：
--
作者：
Nielsen, Ronni;Pedersen, Thomas Askov;Stunnenberg, Hendrik G.
核受体过氧化物酶体增殖物激活受体γ（PPAR γ）是体内和离体脂肪细胞分化的关键调节剂，并且已显示控制几种脂肪细胞特异性基因的表达。在这项研究中，我们使用染色质免疫沉淀结合深度测序，以非常高的分辨率在整个3 T3-L1细胞的脂肪细胞分化过程中生成全基因组范围的PPAR γ和类维生素A X受体（RXR）结合位点的图谱，以及RNA聚合酶II（RNAPII）占有率。我们在脂肪细胞中鉴定了> 5000个高置信度共享的PPARgamma：RXR结合位点，并表明在分化的早期阶段，其中许多被非PPARgamma RXR异二聚体占据。不同的时间和组成模式的占用观察。此外，我们还检测到与C/EBP家族成员的共同占有。RNAPII占有率的分析揭示了不同生物过程的相似调控基因的不同簇。PPARgamma：RXR结合与大多数诱导基因相关，并且位点在涉及脂质和葡萄糖代谢的基因附近特别丰富。我们的分析代表了第一个全基因组范围内的地图的PPAR γ：RXR靶位点和RNAPII占用整个脂肪细胞分化的变化，并表明，迄今尚未认识到的大量脂肪细胞基因的明显调控途径是直接激活的PPAR γ：RXR。
The nuclear receptor peroxisome proliferator-activated receptor gamma(PPAR gamma) is a key regulator of adipocyte differentiation in vivo and ex vivo and has been shown to control the expression of several adipocyte-specific genes. In this study, we used chromatin immunoprecipitation combined with deep sequencing to generate genome-wide maps of PPAR gamma and retinoid X receptor (RXR)-binding sites, and RNA polymerase II (RNAPII) occupancy at very high resolution throughout adipocyte differentiation of 3T3-L1 cells. We identify > 5000 high-confidence shared PPAR gamma:RXR-binding sites in adipocytes and show that during early stages of differentiation, many of these are preoccupied by non-PPAR gamma RXR-heterodimers. Different temporal and compositional patterns of occupancy are observed. In addition, we detect co-occupancy with members of the C/EBP family. Analysis of RNAPII occupancy uncovers distinct clusters of similarly regulated genes of different biological processes. PPAR gamma:RXR binding is associated with the majority of induced genes, and sites are particularly abundant in the vicinity of genes involved in lipid and glucose metabolism. Our analyses represent the first genome-wide map of PPAR gamma:RXR target sites and changes in RNAPII occupancy throughout adipocyte differentiation and indicate that a hitherto unrecognized high number of adipocyte genes of distinctly regulated pathways are directly activated by PPAR gamma:RXR.