Combined ChIP-Seq and transcriptome analysis identifies AP-1/JunD as a primary regulator of oxidative stress and IL-1β synthesis in macrophages

BMC Genomics. 2013 Feb 11;14:92. doi: 10.1186/1471-2164-14-92.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Gene Expression / drug effects
  • Gene Expression Profiling
  • Glomerulonephritis / chemically induced
  • Glomerulonephritis / genetics
  • Glomerulonephritis / metabolism
  • Glomerulonephritis / pathology
  • Interleukin-1beta / biosynthesis
  • Interleukin-1beta / genetics
  • Interleukin-1beta / metabolism*
  • Lipopolysaccharides / toxicity
  • Macrophages / cytology
  • Macrophages / drug effects
  • Macrophages / metabolism*
  • Oxidative Stress / genetics*
  • Primary Cell Culture
  • Protein Binding
  • Proto-Oncogene Proteins c-jun* / genetics
  • Proto-Oncogene Proteins c-jun* / metabolism
  • Rats
  • Transcription Factor AP-1* / genetics
  • Transcription Factor AP-1* / metabolism

Substances

  • Interleukin-1beta
  • JunD protein, rat
  • Lipopolysaccharides
  • Proto-Oncogene Proteins c-jun
  • Transcription Factor AP-1