SATB1 targets chromatin remodelling to regulate genes over long distances

Eukaryotic chromosomes are organized inside the nucleus in such a way that only a subset of the genome is expressed in any given cell type, but the details of this organization are largely unknown1,2,3. SATB1 (‘special AT-rich sequence binding 1’), a protein found predominantly in thymocytes4, regulates genes by folding chromatin into loop domains, tethering specialized DNA elements to an SATB1 network structure5. Ablation of SATB1 by gene targeting results in temporal and spatial mis-expression of numerous genes and arrested T-cell development, suggesting that SATB1 is a cell-type specific global gene regulator6. Here we show that SATB1 targets chromatin remodelling to the IL-2Rα (‘interleukin-2 receptor α’) gene, which is ectopically transcribed in SATB1 null thymocytes. SATB1 recruits the histone deacetylase contained in the NURD chromatin remodelling complex to a SATB1-bound site in the IL-2Rα locus, and mediates the specific deacetylation of histones in a large domain within the locus. SATB1 also targets ACF1 and ISWI, subunits of CHRAC and ACF nucleosome mobilizing complexes, to this specific site and regulates nucleosome positioning over seven kilobases. SATB1 defines a class of transcriptional regulators that function as a ‘landing platform’ for several chromatin remodelling enzymes and hence regulate large chromatin domains.