title: Genome-wide identification of hypoxia-inducible factor-1 and -2 binding sites in hypoxic human macrophages alternatively activated by IL-10.
abstract: Macrophages (MΦ) often accumulate in hypoxic areas, where they significantly influence disease progression. Anti-inflammatory cytokines, such as IL-10, generate alternatively activated macrophages that support tumor growth. To understand how alternative activation affects the transcriptional profile of hypoxic macrophages, we globally mapped binding sites of hypoxia-inducible factor (HIF)-1α and HIF-2α in primary human monocyte-derived macrophages prestimulated with IL-10. 713 HIF-1 and 795 HIF-2 binding sites were identified under hypoxia. Pretreatment with IL-10 altered the binding pattern, with 120 new HIF-1 and 188 new HIF-2 binding sites emerging. HIF-1 binding was most prominent in promoters, while HIF-2 binding was more abundant in enhancer regions. Comparison of ChIP-seq data obtained in other cells revealed a highly cell type specific binding of HIF. In MΦ HIF binding occurred preferentially in already active enhancers or promoters. To assess the roles of HIF on gene expression, primary human macrophages were treated with siRNA against HIF-1α or HIF-2α, followed by genome-wide gene expression analysis. Comparing mRNA expression to the HIF binding profile revealed a significant enrichment of hypoxia-inducible genes previously identified by ChIP-seq. Analysis of gene expression under hypoxia alone and hypoxia/IL-10 showed the enhanced induction of a set of genes including PLOD2 and SLC2A3, while another group including KDM3A and ADM remained unaffected or was reduced by IL-10. Taken together IL-10 influences the DNA binding pattern of HIF and the level of gene induction.
authors.affiliation: Institute of Biochemistry I/ZAFES, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Tausendschön
authors.affiliation: Department of Internal Medicine III, University Hospital Regensburg, 95053 Regensburg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Rehli
authors.affiliation: Institute of Biochemistry I/ZAFES, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany. Electronic address: dehne@biochem.uni-frankfurt.de.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Dehne
authors.affiliation: Department of Internal Medicine III, University Hospital Regensburg, 95053 Regensburg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Schmidl
authors.affiliation: Institute of Pathology, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Döring
authors.affiliation: Institute of Pathology, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany.
authors.forename: Martin-Leo
authors.initials: ML
authors.lastname: Hansmann
authors.affiliation: Institute of Biochemistry I/ZAFES, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Brüne
mesh_terms: D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D015687:Cell Hypoxia / Q000235:genetics*; D005786:Gene Expression Regulation; D015894:Genome, Human; D051274:Glucose Transporter Type 3 / Q000096:biosynthesis; D006801:Humans; D051795:Hypoxia-Inducible Factor 1, alpha Subunit / Q000235:genetics* / Q000378:metabolism; D016753:Interleukin-10 / Q000008:administration & dosage / Q000378:metabolism*; D008264:Macrophages / Q000378:metabolism / Q000473:pathology; D008240:Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase / Q000096:biosynthesis; D000099162:Endothelial PAS Domain-Containing Protein 1
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D051274:Glucose Transporter Type 3; D051795:Hypoxia-Inducible Factor 1, alpha Subunit; D016753:Interleukin-10; D008240:Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase; D000099162:Endothelial PAS Domain-Containing Protein 1; C495687:SLC2A3 protein, human; C479138:PLOD2 protein, human
keywords: ChIP-seq; Enhancer; Hypoxia; Promoter