Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells

Andreas Jeron12*, Wiebke Hansen3, Franziska Ewert2, Jan Buer3, Robert Geffers4* and Dunja Bruder12

Author Affiliations

1 Immune Regulation group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany

2 Infection Immunology group, Institute of Medical Microbiology, Faculty of Medicine, Otto-von-Guericke University Magdeburg, Leipziger Straße 44, Magdeburg, 39120, Germany

3 Institute of Medical Microbiology, University Hospital Essen, Hufelandstraße 55, Essen, 45122, Germany

4 Genome Analytics group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany

For all author emails, please log on.

BMC Genomics 2012, 13:705  doi:10.1186/1471-2164-13-705

Published: 17 December 2012

Abstract

Background

The transcription factor (TF) forkhead box P3 (FOXP3) is constitutively expressed at high levels in naturally occurring CD4+CD25+ regulatory T cells (nTregs). It is not only the most accepted marker for that cell population but is also considered lineage determinative. Chromatin immunoprecipitation (ChIP) of TFs in combination with genomic tiling microarray analysis (ChIP-on-chip) has been shown to be an appropriate tool for identifying FOXP3 transcription factor binding sites (TFBSs) on a genome-wide scale. In combination with microarray expression analysis, the ChIP-on-chip technique allows identification of direct FOXP3 target genes.

Results

ChIP-on-chip analysis of the human FOXP3 expressed in resting and PMA/ionomycin–stimulated Jurkat T cells revealed several thousand putative FOXP3 binding sites and demonstrated the importance of intronic regions for FOXP3 binding. The analysis of expression data showed that the stimulation-dependent down-regulation of IL-22 was correlated with direct FOXP3 binding in the IL-22 promoter region. This association was confirmed by real-time PCR analysis of ChIP-DNA. The corresponding ChIP-region also contained a matching FOXP3 consensus sequence.

Conclusions

Knowledge of the general distribution patterns of FOXP3 TFBSs in the human genome under resting and activated conditions will contribute to a better understanding of this TF and its influence on direct target genes, as well as its importance for the phenotype and function of Tregs. Moreover, FOXP3-dependent repression of Th17-related IL-22 may be relevant to an understanding of the phenomenon of Treg/Th17 cell plasticity.

Keywords:
FOXP3; ChIP-on-chip; Jurkat T cells; Transcription factor binding sites; IL-22