DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions

Nucleic Acids Res. 2015 Jan;43(2):1268-82. doi: 10.1093/nar/gku1373. Epub 2015 Jan 7.

Abstract

FOXP3 is a lineage-specific transcription factor that is required for regulatory T cell development and function. In this study, we determined the crystal structure of the FOXP3 forkhead domain bound to DNA. The structure reveals that FOXP3 can form a stable domain-swapped dimer to bridge DNA in the absence of cofactors, suggesting that FOXP3 may play a role in long-range gene interactions. To test this hypothesis, we used circular chromosome conformation capture coupled with high throughput sequencing (4C-seq) to analyze FOXP3-dependent genomic contacts around a known FOXP3-bound locus, Ptpn22. Our studies reveal that FOXP3 induces significant changes in the chromatin contacts between the Ptpn22 locus and other Foxp3-regulated genes, reflecting a mechanism by which FOXP3 reorganizes the genome architecture to coordinate the expression of its target genes. Our results suggest that FOXP3 mediates long-range chromatin interactions as part of its mechanisms to regulate specific gene expression in regulatory T cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosomes / chemistry*
  • DNA / chemistry*
  • DNA / metabolism
  • Forkhead Transcription Factors / chemistry*
  • Forkhead Transcription Factors / metabolism
  • Gene Expression Regulation
  • Humans
  • Mice, Inbred C57BL
  • Models, Molecular
  • Protein Multimerization
  • Protein Structure, Tertiary
  • Protein Tyrosine Phosphatase, Non-Receptor Type 22 / genetics

Substances

  • FOXP3 protein, human
  • Forkhead Transcription Factors
  • DNA
  • Protein Tyrosine Phosphatase, Non-Receptor Type 22

Associated data

  • PDB/4WK8
  • SRA/SRS794839
  • SRA/SRS794865