An intron transcriptional enhancer element regulates IL-4 gene locus accessibility in mast cells

A 3' enhancer in the IL-4 gene regulates cytokine production by Th2 cells and mast cells

Differentiation of naive T cells into mature Th2 cells is associated with the appearance of a complex pattern of DNase I hypersensitive (DH) sites within the IL-4/IL-13 cytokine gene cluster. We show here that targeted deletion of an inducible DH site, V(A), and the adjacent conserved DH site V (CNS-2) selectively compromises IL-4 gene transcription by differentiated Th2 cells and mast cells. In mast cells, the deletion abrogates IL-4 mRNA induction, an effect mimicked by deletion of the transcription factor NFAT1 (NFATc2), which binds DH site V(A). In T cells, the deletion impairs a process of response maturation, defined by progressive increases in IL-4 levels as Th2 differentiation proceeds. These results identify an essential enhancer which regulates IL-4 gene expression in two important cell lineages in vivo.

Th2 lineage commitment and efficient IL-4 production involves extended demethylation of the IL-4 gene

The relation of CpG methylation to gene silencing is well established, but the contribution of DNA demethylation to gene expression during cell differentiation remains unclear. We show that the IL-4 locus undergoes a complex series of methylation and demethylation steps during T helper cell differentiation. The 5' region of the IL-4 locus is hypermethylated in naive T cells and becomes specifically demethylated in Th2 cells, whereas a highly conserved DNase I-hypersensitive region at the 3' end shows the converse behavior, being hypomethylated in naive T cells and becoming methylated during Th1 differentiation. 5' demethylation is not required for chromatin remodeling or primary transcription of the IL-4 gene but is strongly associated with efficient, high-level induction of IL-4 transcripts by differentiated Th2 cells.

A region in the first exon/intron of rat carnitine palmitoyltransferase Ibeta is involved in enhancement of basal transcription

Carnitine palmitoyltransferase-Ibeta (CPT-Ibeta) catalyses the transfer of long-chain fatty acids to the enzymes of beta-oxidation of muscle and heart. Transcriptional control of this regulatory protein is relevant to disorders of fatty acid oxidation and the switch to glucose metabolism that occurs in cardiac pathology. The presence of a transcriptional enhancer sequence in the first untranslated exon and first intron of the CPT-Ibeta gene was identified using deletional and mutational analysis, and by ligation of an oleate responsive element (fatty acid response element) to a minimal promoter. The enhancer sequences are contained in the first 40 bases downstream of the transcription start site and increase CPT-Ibeta reporter gene expression independent of any 5' cis-acting elements. Deletion of the first 40 bases of the 3'-untranslated region does not affect the up-regulation of transcription by 10 microM phenylephrine. However, mutation and/or deletion of bases between +11 and +30 dramatically decreases reporter gene expression. Electrophoretic mobility-shift assays reveal two DNA (+11 to +36)-protein complexes that appear cardiac specific. The exon/intron element enhances activation of the heterologous thymidine kinase promoter in a position- and orientation-dependent manner. Therefore we have identified a novel region in the first exon/intron of the CPT-Ibeta gene that acts as a non-classical transcriptional enhancer downstream of regulatory elements characterized previously in the 5'-flanking region of the minimal promoter.

The functional genomics of CD14 and its role in IgE responses: an integrated view

Several studies in recent years have suggested that there is a strong genetic component in the pathogenesis of IgE-mediated diseases. Epidemiologic studies have identified a number of genes that carry single base changes (single nucleotide polymorphisms) associated with parameters of allergy. What remain to be established are the mechanisms whereby genetic variation results in dysregulation of IgE-mediated responses. This is the task of functional genomics. In this article, some of the most powerful approaches that have been devised to provide a mechanistic explanation for the effects of genetic variation on the regulation of gene expression and function are discussed. Recent data on the impact of genetic variation on the regulation of CD14 are explored in the context of the potential role played by this gene in the pathogenesis of allergy. Also discussed is the notion that taken individually, each instance of variation might result in small effects. It is the combination of variations in the same gene and/or in genes arrayed along one functional pathway that might eventually lead to dysregulation strong enough to cause disease. In this scenario, the environment is likely to play an essential role in determining the functional outcome of genetic variation.

Deletion of a coordinate regulator of type 2 cytokine expression in mice

Mechanisms that underlie the patterning of cytokine expression in T helper (T(H)) cell subsets remain incompletely defined. An evolutionarily conserved approximately 400-bp noncoding sequence in the intergenic region between the genes Il4 and Il13, designated conserved noncoding sequence 1 (CNS-1), was deleted in mice. The capacity to develop T(H)2 cells was compromised in vitro and in vivo in the absence of CNS-1. Despite the profound effect in T cells, mast cells from CNS-1(-/-) mice maintained their capacity to produce interleukin 4. A T cell-specific element critical for the optimal expression of type 2 cytokines may represent the evolution of a regulatory sequence exploited by adaptive immunity.

Regulation of IL-4 gene expression by distal regulatory elements and GATA-3 at the chromatin level

Using a transgenic approach, we examined distal regulatory elements located in the IL-4 locus and the role of GATA-3 at these elements. The intergenic DNase I hypersensitive sites (HSS) showed strong enhancement, and the intronic enhancer (IE) and HS5/HS5a sites showed weaker enhancement of the IL-4 promoter. Elements in the 3' region of the IL-4 gene contributed to Th2 specificity. All individual enhancers were T cell activation dependent but not Th2 specific, with the exception of IE. However, when these distal elements were combined into a "minilocus," expression was strongly enhanced and Th2 specific. GATA-3 mediated strong enhancement of IL-4 promoter activity in Th1 cells when the promoter was embedded in the minilocus or linked to HSS and IE, demonstrating that GATA-3 acts through these elements to regulate IL-4 gene expression.