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

Nature Genetics volume 38, pages 1278–1288 (2006)Cite this article

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 (TH2) cytokine locus on mouse chromosome 11. We show that on TH2 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 TH2-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 TH2 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 TH2 cell activation.

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Figure 1: Upon D10.G4.1 (TH2) cell activation, SATB1 expression is induced, and cytokine expression levels increase.
Figure 2: ChIP analysis of the TH2 cytokine locus in D10.G4.1 (TH2) cells uncovers SATB1 binding sequences (SBSs).
Figure 3: Chromatin loop analyses from SBS-C1 and SBS-C9 show dense SATB1-bound chromatin looping upon D10.G4.1 activation.
Figure 4: Rad50 intronic SBSs contribute to chromatin loop organization of TH2 cytokine locus in D10.G4.1 cells.
Figure 5: TH2 cytokine gene promoters are juxtaposed on D10.G4.1 activation, but the Rad50 promoter is not involved.
Figure 6: Association of TH2-specific factors, RNA polymerase II, Brg1 and acetylated histone H3 with the cytokine region.
Figure 7: SATB1 is required for Il4, Il5 and Il13 expression, induction of c-Maf and dense looping of active chromatin upon TH2 cell activation.
Figure 8: Summary of activation-dependent looping events and a model of transcriptionally active chromatin.

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Acknowledgements

We thank N. Arai and S. Miyatake for instructing us on culturing D10.G4.1 cells, M. Kohwi for critically reading the manuscript and M. Miyano for drawing the loop model. This work was supported by US National Institutes of Health grants to T.K.-S.

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Authors and Affiliations

  1. Lawrence Berkeley Laboratory, University of California, Berkeley, 94720, California, USA

    Shutao Cai, Charles C Lee & Terumi Kohwi-Shigematsu

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Contributions

All data shown in Figures 1, 2, 3, 4, 5, 6, 7 were produced by S.C., except for cloning of the nine SBSs, which was performed by C.C.L. This paper was written by T.K.-S. and S.C. This study was designed by T.K.-S.

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Correspondence to Terumi Kohwi-Shigematsu.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Cloning of genomic sequences that bind to SATB1 in vitro. (PDF 196 kb)

Supplementary Fig. 2

ChIP loop assay and 3C assay to determine chromatin structure of the TH2 cytokine locus. (PDF 2640 kb)

Supplementary Fig. 3

Primer sequences and DNA fragment sizes. (PDF 2079 kb)

Supplementary Fig. 4

Immunolocalization of RNA polymerase II, c-Maf, STAT6, Brg1 and SATB1 in resting and activated D10.G4.1 cells. (PDF 766 kb)

Supplementary Fig. 5

FISH analysis for the 200-kb cytokine region. (PDF 235 kb)

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Cai, S., Lee, C. & Kohwi-Shigematsu, T. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet 38, 1278–1288 (2006). https://doi.org/10.1038/ng1913

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