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

  1. Ronni Nielsen1,4,
  2. Thomas Åskov Pedersen1,4,
  3. Dik Hagenbeek2,4,
  4. Panagiotis Moulos2,3,
  5. Rasmus Siersbæk1,
  6. Eva Megens2,
  7. Sergei Denissov2,
  8. Michael Børgesen1,
  9. Kees-Jan Francoijs2,
  10. Susanne Mandrup1,6, and
  11. Hendrik G. Stunnenberg2,5
  1. 1 Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark;
  2. 2 Department of Molecular Biology, Nijmegen Center for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands;
  3. 3 Metabolic Engineering and Bioinformatics Group, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece
  1. 4 These authors contributed equally to this work.

Abstract

The nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) 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 PPARγ 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 PPARγ:RXR-binding sites in adipocytes and show that during early stages of differentiation, many of these are preoccupied by non-PPARγ 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. PPARγ: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 PPARγ: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 PPARγ:RXR.

Keywords

Footnotes

| Table of Contents

Life Science Alliance