title: Combined ChIP-Seq and transcriptome analysis identifies AP-1/JunD as a primary regulator of oxidative stress and IL-1β synthesis in macrophages.
abstract: BACKGROUND
  The oxidative burst is one of the major antimicrobial mechanisms adopted by macrophages. The WKY rat strain is uniquely susceptible to experimentally induced macrophage-dependent crescentic glomerulonephritis (Crgn). We previously identified the AP-1 transcription factor JunD as a determinant of macrophage activation in WKY bone marrow-derived macrophages (BMDMs). JunD is over-expressed in WKY BMDMs and its silencing reduces Fc receptor-mediated oxidative burst in these cells.
  
  
  RESULTS
  Here we combined Jund RNA interference with microarray analyses alongside ChIP-sequencing (ChIP-Seq) analyses in WKY BMDMs to investigate JunD-mediated control of macrophage activation in basal and lipopolysaccharide (LPS) stimulated cells. Microarray analysis following Jund silencing showed that Jund activates and represses gene expression with marked differential expression (>3 fold) for genes linked with oxidative stress and IL-1β expression. These results were complemented by comparing whole genome expression in WKY BMDMs with Jund congenic strain (WKY.LCrgn2) BMDMs which express lower levels of JunD. ChIP-Seq analyses demonstrated that the increased expression of JunD resulted in an increased number of binding events in WKY BMDMs compared to WKY.LCrgn2 BMDMs. Combined ChIP-Seq and microarray analysis revealed a set of primary JunD-targets through which JunD exerts its effect on oxidative stress and IL-1β synthesis in basal and LPS-stimulated macrophages.
  
  
  CONCLUSIONS
  These findings demonstrate how genetically determined levels of a transcription factor affect its binding sites in primary cells and identify JunD as a key regulator of oxidative stress and IL-1β synthesis in primary macrophages, which may play a role in susceptibility to Crgn.
authors: MRC Clinical Sciences Centre, Imperial College London, Hammersmithhospital, Du Cane Road W12 0NN, London, UK.
authors: Richard P
authors: RP
authors: Hull
authors: Prashant K
authors: PK
authors: Srivastava
authors: Zelpha
authors: Z
authors: D'Souza
authors: Santosh S
authors: SS
authors: Atanur
authors: Fatima
authors: F
authors: Mechta-Grigoriou
authors: Laurence
authors: L
authors: Game
authors: Enrico
authors: E
authors: Petretto
authors: H Terence
authors: HT
authors: Cook
authors: Timothy J
authors: TJ
authors: Aitman
authors: Jacques
authors: J
authors: Behmoaras
mesh_terms: D000818:Animals; D001665:Binding Sites; D015870:Gene Expression / Q000187:drug effects; D020869:Gene Expression Profiling; D005921:Glomerulonephritis / Q000139:chemically induced / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D053583:Interleukin-1beta / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D008070:Lipopolysaccharides / Q000633:toxicity; D008264:Macrophages / Q000166:cytology / Q000187:drug effects / Q000378:metabolism*; D018384:Oxidative Stress / Q000235:genetics*; D061251:Primary Cell Culture; D011485:Protein Binding; D016755:Proto-Oncogene Proteins c-jun / Q000235:genetics / Q000378:metabolism; D051381:Rats; D018808:Transcription Factor AP-1 / Q000235:genetics / Q000378:metabolism
chemical_list: D053583:Interleukin-1beta; C549531:JunD protein, rat; D008070:Lipopolysaccharides; D016755:Proto-Oncogene Proteins c-jun; D018808:Transcription Factor AP-1
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