SATB1 target genes during Th1 and Th2 cell differentiation. (A) Expression profiles of SATB1-siRNA/shRNA and scrambled control siRNA/shRNA-treated cells were studied using Illumina bead arrays. Venn diagram shows the number of genes of which the expression was altered on SATB1 knockdown in each Th subtype. (B) The regulation of SATB1 RNAi target genes by cytokines (IL-12 and/or IL-4) and TCR was determined as described in “SATB1 regulates more than 300 genes in developing Th1 and Th2 cells.” (C) Direct SATB1 target genes are common hits of 2 independent approaches: (1) gene expression profiling of SATB1-siRNA/shRNA-treated cells analyzed using Illumina bead arrays and (2) ChIP-on-chip analysis using SATB1-enriched chromatin from cord blood CD4⁺ T cells polarized to Th1 and Th2 directions for 24 hours. Heat map visualization of direct SATB1 target genes grouped according to their regulation by IL-4, IL-12, and IL-4, T-cell activation (TCR), or none of the above (other). Green represents decreased; and red, increased gene expression (fold change) on SATB1 down-regulation in indicated Th subtypes (Thp, Th0, Th1, or Th2) or across all Th subtypes (Any). *The 2 last columns indicated represent the Th1 or Th2 specific binding of SATB1 detected with ChIP-on-chip approach.