The T-helper-cell 1 and 2 (T(H)1 and T(H)2) pathways, defined by cytokines interferon-gamma (IFN-gamma) and interleukin-4 (IL-4), respectively, comprise two alternative CD4+ T-cell fates, with functional consequences for the host immune system. These cytokine genes are encoded on different chromosomes. The recently described T(H)2 locus control region (LCR) coordinately regulates the T(H)2 cytokine genes by participating in a complex between the LCR and promoters of the cytokine genes Il4, Il5 and Il13. Although they are spread over 120 kilobases, these elements are closely juxtaposed in the nucleus in a poised chromatin conformation. In addition to these intrachromosomal interactions, we now describe interchromosomal interactions between the promoter region of the IFN-gamma gene on chromosome 10 and the regulatory regions of the T(H)2 cytokine locus on chromosome 11. DNase I hypersensitive sites that comprise the T(H)2 LCR developmentally regulate these interchromosomal interactions. Furthermore, there seems to be a cell-type-specific dynamic interaction between interacting chromatin partners whereby interchromosomal interactions are apparently lost in favour of intrachromosomal ones upon gene activation. Thus, we provide an example of eukaryotic genes located on separate chromosomes associating physically in the nucleus via interactions that may have a function in coordinating gene expression.

The T helper type 2 (T(H)2) locus control region is important in the regulation of the genes encoding the cytokines interleukins 4, 5 and 13. Using the chromosome conformation capture technique, we found that in T cells, natural killer cells, B cells and fibroblasts, the promoters for the genes encoding T(H)2 cytokines are located in close spatial proximity, forming an initial chromatin core configuration. In CD4(+) T cells and natural killer cells, but not B cells and fibroblasts, the T(H)2 locus control region participates in this configuration. The transcription factors GATA3 and STAT6 are essential for the establishment and/or maintenance of these interactions. Intrachromosomal interactions in the T(H)2 cytokine locus may form the basis for the coordinated transcriptional regulation of cytokine-encoding genes by the T(H)2 locus control region.

Cytokine loci undergo changes in chromatin structure when naive CD4(+) T cells differentiate into Th1 or Th2 cells and have also been examined for regulatory sequences underlying such changes and their functional correlates. Studies have shown that distal regulatory elements control the Ifng and Th2 cytokine loci and are primary targets for tissue-specific transcription factors, serving as centers for epigenetic changes that mark heritable traits in effector cells. Reports of intra- and, remarkably, interchromosomal interactions between these regulatory elements shed light on the mechanisms by which they regulate gene expression, revealing an extraordinary new picture that conceptually extends our views on how genes are regulated from two to three dimensions. Here, we summarize these recent findings on the role of regulatory elements and their mechanisms of action, which are of broad significance for gene regulation, not only of the immune system but also of many, if not all, coregulated genes.

The class II transactivator (CIITA), the master regulator of the tissue-specific and interferon gammainducible expression of major histocompatibility complex class II genes, synergizes with the histone acetylase coactivator CBP to activate gene transcription. Here we demonstrate that in addition to CBP, PCAF binds to CIITA both in vivo and in vitro and enhances CIITA-dependent transcriptional activation of class II promoters. Accordingly, E1A mutants defective for PCAF or CBP interaction show reduced ability in suppressing CIITA activity. Interestingly, CBP and PCAF acetylate CIITA at lysine residues within a nuclear localization signal. We show that CIITA is shuttling between the nucleus and cytoplasm. The shuttling behavior and activity of the protein are regulated by acetylation: overexpression of PCAF or inhibition of cellular deacetylases by trichostatin A increases the nuclear accumulation of CIITA in a manner determined by the presence of the acetylation target lysines. Furthermore, mutagenesis of the acetylated residues reduces the transactivation ability of CIITA. These results support a novel function for acetylation, i.e., to regulate gene expression by stimulating the nuclear accumulation of an activator.Major histocompatibility complex (MHC) class II genes encode heterodimeric cell surface molecules that are essential for the presentation of foreign antigenic peptides to helper T cells. Human and mouse genes are expressed in antigen-presenting cells as well as in various cell types upon gamma interferon (IFN-␥) stimulation (16, 34, 52). The expression of these genes occurs mainly at the transcriptional level and is regulated by an array of functional cis elements (H/W, X, and Y) that are conserved among all class II genes (16). Transcription of class II genes is orchestrated by the assembly of a higher-order multiprotein complex on the promoter and requires recruitment of the class II transactivator, CIITA (6, 34). Both constitutive and IFN-␥-inducible expression of class II genes are determined by the presence of CIITA in a variety of cell types (8,34,49). Functional analysis of the structure of CIITA revealed the presence of a C-terminal region required for promoter recruitment (44,59) and an N-terminal acidic transactivation domain that can contact the basic transcriptional machinery (13,35).Recently, we and others have demonstrated that the histone acetylase CREB binding protein (CBP) interacts with CIITA and functions as a coactivator for both B-cell-specific and IFN-␥-induced transcription of MHC class II genes (13, 30). Consequently, expression of MHC class II genes was suppressed by the adenovirus E1A protein (30), which is known to strongly bind to and inhibit CBP action (1, 33).The discovery that transcriptional coactivators have histone acetylase activity (4, 41) provided important insights into the process that links chromatin acetylation to transcriptional activation (20,31,50). CBP/p300 and the associated factor PCAF collaborate with many transcription factors as well as with other coa...