Chromatin loop organization of the junb locus in mouse dendritic cells

Nucleic Acids Res. 2013 Oct;41(19):8908-25. doi: 10.1093/nar/gkt669. Epub 2013 Aug 5.


The junb gene behaves as an immediate early gene in bacterial lipopolysaccharide (LPS)-stimulated dendritic cells (DCs), where its transient transcriptional activation is necessary for the induction of inflammatory cytokines. junb is a short gene and its transcriptional activation by LPS depends on the binding of NF-κB to an enhancer located just downstream of its 3' UTR. Here, we have addressed the mechanisms underlying the transcriptional hyper-reactivity of junb. Using transfection and pharmacological assays to complement chromatin immunoprecipitation analyses addressing the localization of histones, polymerase II, negative elongation factor (NELF)-, DRB sensitivity-inducing factor (DSIF)- and Positive Transcription Factor b complexes, we demonstrate that junb is a RNA Pol II-paused gene where Pol II is loaded in the transcription start site domain but poorly active. Moreover, High salt-Recovered Sequence, chromosome conformation capture (3C)- and gene transfer experiments show that (i) junb is organized in a nuclear chromatin loop bringing into close spatial proximity the upstream promoter region and the downstream enhancer and (ii) this configuration permits immediate Pol II release on the junb body on binding of LPS-activated NF-κB to the enhancer. Thus, our work unveils a novel topological framework underlying fast junb transcriptional response in DCs. Moreover, it also points to a novel layer of complexity in the modes of action of NF-κB.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Chromatin / chemistry*
  • Dendritic Cells / chemistry
  • Dendritic Cells / enzymology
  • Dendritic Cells / metabolism*
  • Enhancer Elements, Genetic
  • Genetic Loci
  • Histones / analysis
  • Humans
  • Lipopolysaccharides / pharmacology
  • Mice
  • Nucleic Acid Conformation
  • RNA Polymerase II / analysis
  • Transcription Factors / biosynthesis
  • Transcription Factors / genetics*
  • Transcription Initiation Site
  • Transcriptional Activation*


  • Chromatin
  • Histones
  • JunB protein, mouse
  • Lipopolysaccharides
  • Transcription Factors
  • RNA Polymerase II