SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes

Nat Genet. 2006 Nov;38(11):1278-88. doi: 10.1038/ng1913. Epub 2006 Oct 22.

Abstract

SATB1 (special AT-rich sequence binding protein 1) organizes cell type-specific nuclear architecture by anchoring specialized DNA sequences and recruiting chromatin remodeling factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4 and Il13, located in the 200-kb T-helper 2 (T(H)2) cytokine locus on mouse chromosome 11. We show that on T(H)2 cell activation, SATB1 expression is rapidly induced to form a unique transcriptionally active chromatin structure at the cytokine locus. In this structure, chromatin is folded into numerous small loops, all anchored to SATB1 at their base. In addition, histone H3 is acetylated at Lys9 and Lys14, and the T(H)2-specific factors GATA3, STAT6 and c-Maf, the chromatin-remodeling enzyme Brg1 and RNA polymerase II are all bound across the 200-kb region. Before activation, the T(H)2 cytokine locus is already associated with GATA3 and STAT6, showing some looping, but these are insufficient to induce cytokine gene expression. Using RNA interference, we show that on cell activation, SATB1 is required not only for compacting chromatin into dense loops at the 200-kb cytokine locus but also for inducing Il4, Il5, Il13 and c-Maf expression. Thus, SATB1 is a necessary determinant for the hitherto unidentified higher-order, transcriptionally active chromatin structure that forms on T(H)2 cell activation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Acetylation
  • Acid Anhydride Hydrolases
  • Animals
  • Binding Sites
  • Chromatin / chemistry*
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation / methods
  • Chromosomes / chemistry
  • Cytokines / metabolism*
  • DNA Helicases / metabolism
  • DNA Repair Enzymes / genetics
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / physiology
  • GATA3 Transcription Factor / metabolism
  • Gene Expression Regulation
  • Histone Acetyltransferases / metabolism
  • Histones / metabolism
  • Locus Control Region
  • Lymphocyte Activation / physiology
  • Matrix Attachment Region Binding Proteins / physiology*
  • Mice
  • Mice, Inbred AKR
  • Models, Biological
  • Nuclear Proteins / metabolism
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic
  • Proto-Oncogene Proteins c-maf / metabolism
  • RNA Polymerase II / metabolism
  • STAT6 Transcription Factor / metabolism
  • Th2 Cells / metabolism
  • Transcription Factors / metabolism
  • Transcription, Genetic / physiology*

Substances

  • Chromatin
  • Cytokines
  • DNA-Binding Proteins
  • GATA3 Transcription Factor
  • Gata3 protein, mouse
  • Histones
  • Maf protein, mouse
  • Matrix Attachment Region Binding Proteins
  • Nuclear Proteins
  • Proto-Oncogene Proteins c-maf
  • STAT6 Transcription Factor
  • Satb1 protein, mouse
  • Stat6 protein, mouse
  • Transcription Factors
  • Histone Acetyltransferases
  • RNA Polymerase II
  • Acid Anhydride Hydrolases
  • Rad50 protein, human
  • Smarca4 protein, mouse
  • DNA Helicases
  • DNA Repair Enzymes