title: Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis.
abstract: The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma) 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 PPARgamma 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 PPARgamma:RXR-binding sites in adipocytes and show that during early stages of differentiation, many of these are preoccupied by non-PPARgamma 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. PPARgamma: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 PPARgamma: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 PPARgamma:RXR.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
authors.forename: Ronni
authors.initials: R
authors.lastname: Nielsen
authors.forename: Thomas Askov
authors.initials: TA
authors.lastname: Pedersen
authors.forename: Dik
authors.initials: D
authors.lastname: Hagenbeek
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Moulos
authors.forename: Rasmus
authors.initials: R
authors.lastname: Siersbaek
authors.forename: Eva
authors.initials: E
authors.lastname: Megens
authors.forename: Sergei
authors.initials: S
authors.lastname: Denissov
authors.forename: Michael
authors.initials: M
authors.lastname: Børgesen
authors.forename: Kees-Jan
authors.initials: KJ
authors.lastname: Francoijs
authors.forename: Susanne
authors.initials: S
authors.lastname: Mandrup
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
mesh_terms: D041721:3T3-L1 Cells; D017667:Adipocytes / Q000166:cytology / Q000378:metabolism; D050156:Adipogenesis / Q000502:physiology*; D000818:Animals; D019281:Dimerization; D016678:Genome; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family; D047495:PPAR gamma / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism*; D047488:Retinoid X Receptors / Q000378:metabolism*
chemical_list: D047495:PPAR gamma; D047488:Retinoid X Receptors; D012319:RNA Polymerase II