Induction of histone H4 acetylation at the IFNG locus. (A) Chromosomal DNA was prepared from naive or memory T cells isolated from human peripheral blood and from cells of a human iNKT clonal line that were either rested or stimulated with PMA and ionomycin and subject to ChIP-chip analysis of IFNG locus histone H4 acetylation. The tracks show log₂ ratios of fluorescence from acetylated histone H4 immunoprecipitates compared with input DNA. Regions highlighted in red represent statistically significant signal (false discovery rate P < 0.05). Results shown are from a single analysis in which all of the samples were processed in parallel; similar results were obtained in two additional independent analyses. (B) Analysis of the IFNG locus of an iNKT clone that was rested (top track) compared with when it was exposed to CD1d⁺ APCs for 4 h (middle track). Shown on the bottom track is the net increase in acetylated histone H4 signal from the preexposed compared with the rested iNKT cells. Results shown are from one representative analysis out of three independent experiments. (C) mVista analysis of chromosomal sequence identity for this region of the human and mouse IFNG gene loci. Pink shaded areas indicate conserved noncoding sequences (CNS) identified by the mVista software, and blue shaded areas designate exons from the IFNG gene. The two areas highlighted in purple show regions that have been identified in the mouse IFNG gene locus as containing specific conserved noncoding sequences (mCNS1 or mCNS2) that have enhancer activity (Lee et al., 2004; Shnyreva et al., 2004). (D) ChIP-chip analysis of regions of chromosome 5 that contain genes encoding the cytokines IL-3 (IL3), GM-CSF (CSF2), IL-13 (IL13), and IL-4 (IL4). Results shown are from a single analysis in which all of the samples were processed in parallel; similar results were obtained in two additional independent analyses. (E) ChIP-chip analysis of the IL-2 locus. Results shown are from a single analysis in which all of the samples were processed in parallel; similar results were obtained in two additional independent analyses.