We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP‐seq) and DNase‐seq data (n > 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a data‐mining platform—designated ChIP‐Atlas (http://chip-atlas.org). ChIP‐Atlas is able to show alignment and peak‐call results for all public ChIP‐seq and DNase‐seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature. All peak‐call data are integrated to visualize multiple histone modifications and binding sites of transcriptional regulators (TRs) at given genomic loci. The integrated data can be further analyzed to show TR–gene and TR–TR interactions, as well as to examine enrichment of protein binding for given multiple genomic coordinates or gene names. ChIP‐Atlas is superior to other platforms in terms of data number and functionality for data mining across thousands of ChIP‐seq experiments, and it provides insight into gene regulatory networks and epigenetic mechanisms.

Interleukin (IL)-18 was identified as a molecule that induces IFN-␥ production and enhances NK cell cytotoxicity. In this paper, we report upon the purification and characterization of human IL-18 receptor (hIL-18R). We selected the Hodgkin's disease cell line, L428, as the most strongly hIL-18R-expressing cell line based on the results of binding assays. Murine interleukin-18 (mIL-18) 1 was identified in the livers of mice sequentially injected with heat-killed Propionibacterium acnes and with lipopolysaccharide (1). Murine IL-18 cDNA was cloned from murine liver mRNA, and the factor was provisionally termed IFN-␥-inducing factor because it was first identified as an IFN-␥ inducer in mice. Consequently, human interleukin-18 (hIL-18) was cloned from normal human liver mRNA (2). IL-18 is a non-N-linked, glycosylated, 18.3-kDa cytokine in its mature form and exhibits biologic activities in the monomeric form.IL-18 has been found to have a variety of biologic actions, including the stimulation of the proliferation of activated T cells, enhancement of the lytic activity of NK cells, induction of interferon-␥ (IFN-␥), and granulocyte-macrophage colony-stimulating factor production by activated T cells and promotion of Th1-type helper (Th1) clone responses (1-4). It has also been reported that IL-18 inhibits osteoclast-like multinucleated cell formation in co-cultures of osteoblasts and hemopoietic cells of spleen or bone marrow origin (5). Thus, it is very obvious that IL-18 plays an important role in the immune system.IL-18 shares some of its biologic activities with IL-12, although the primary structures of the two cytokines show no homology (2). In addition, in the experiments using murine Th1 clones and enriched human T cells, IL-18 and IL-12 acted on the T cells synergistically to induce IFN-␥ production (1, 4). Interestingly, the amino acid sequence of IL-18 includes the IL-1 signature-like sequence (2) and has been shown to have 15% homology at the amino acid level with the IL-1␤ protein, but does not bear significant functional resemblance to the IL-1 family (2).The identification of the receptor for IL-18 is important for investigation of the physiological role of IL-18 in nature. In this report, we describe the purification and identification of hIL-18R from a Hodgkin's disease-derived cell line, L428, and present some characterization of this molecule. EXPERIMENTAL PROCEDURES Cell Lines and ReagentsC5/MJ, CCRF-HSB-2, HPB-ALL, JM, MOLT-3, MOLT-4, MOLT-16, PEER, SKW-3 (human T cell leukemia), ARH-77, BALL-1 (human B cell leukemia), KG-1, HL-60, U-937 (human myelomonocytic cell leukemia), NALM-16, HEL (human non-T, non-B cell leukemia), and L-428 and HDLM (human Hodgkin's disease) cell lines were maintained in culture at 37°C, in a 5% CO 2 air mixture in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (BioWhittaker Inc.). Recombinant human IL-1␤ (R&D Systems) and 125 -I-IL-1␤ (Amersham) were obtained commercially. Recombinant IL-18Recombinant human IL-18 (rhIL-18) was produced by cu...

IL-12 and IL-18 synergistically enhance IFN-γ mRNA transcription by activating STAT4 and AP-1, respectively. However, it is still unknown how STAT4/AP-1 elicit IFN-γ promoter activation. Using an IL-12/IL-18-responsive T cell clone, we investigated the mechanisms underlying synergistic enhancement of IFN-γ mRNA expression induced by these two cytokines. Synergy was observed in a reporter gene assay using an IFN-γ promoter fragment that binds AP-1, but not STAT4. An increase in c-Jun, a component of AP-1, in the nuclear compartment was elicited by stimulation with either IL-12 or IL-18, but accumulation of serine-phosphorylated c-Jun was induced only by IL-18 capable of activating c-Jun N-terminal kinase. The binding of AP-1 to the relevant promoter sequence depended on the presence of STAT4. STAT4 bound with c-Jun, and a phosphorylated c-Jun-STAT4 complex most efficiently interacted with the AP-1-relevant promoter sequence. Enhanced cobinding of STAT4 and c-Jun to the AP-1 sequence was also observed when activated lymph node T cells were exposed to IL-12 plus IL-18. These results show that STAT4 up-regulates AP-1-mediated IFN-γ promoter activation without directly binding to the promoter sequence, providing a mechanistic explanation for IL-12/IL-18-induced synergistic enhancement of IFN-γ gene expression.

ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape. ChIP-Atlas is powered by comprehensively integrating all data sets from high-throughput ChIP-seq and DNase-seq, a method for profiling chromatin regions accessible to DNase. In this update, we further collected all the ATAC-seq and whole-genome bisulfite-seq data for six model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast) with the latest genome assemblies. These together with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein–genome interactions. This epigenomic landscape can also be characterized for multiple genes and genomic loci by querying with the Enrichment Analysis tool, which, for example, revealed that inflammatory bowel disease-associated SNPs are the most significantly hypo-methylated in neutrophils. Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All datasets are free to download via either a simple button on the web page or an API.

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