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The Journal of Immunology, 2000, 165: 6687-6691.
Copyright © 2000 by The American Association of Immunologists


CUTTING EDGE

Cutting Edge: Chromatin Remodeling at the IL-4/IL-13 Intergenic Regulatory Region for Th2-Specific Cytokine Gene Cluster1

Naofumi Takemoto*,{dagger}, Yumiko Kamogawa*,{dagger}, Hyun Jun Lee2,{ddagger}, Hirokazu Kurata{ddagger}, Ken-ichi Arai*,{dagger}, Anne O’Garra{ddagger}, Naoko Arai{ddagger} and Shoichiro Miyatake3,*,{dagger}

* Department of Molecular and Developmental Biology, The Institute of Medical Science, University of Tokyo, Tokyo, Japan; {dagger} Core Research for Evolutionary Science and Technology, Saitama, Japan; and {ddagger} Department of Immunology, DNAX Research Institute, Palo Alto, CA 94304


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 References
 
During the differentiation of naive Th cells into Th2 effector cells, the entire IL-4/IL-13 locus is remodeled into an accessible chromatin conformation. Here we show that ectopic expression and activation of Stat6 or GATA-3 in Th cells developing under Th1-polarizing conditions lead to the induction of chromatin remodeling not only at the flanking regions of the IL-4 and IL-13 genes but also at the IL-4/IL-13 intergenic regulatory region for the IL-4/IL-13/IL-5 gene cluster. Furthermore, we demonstrate that GATA-3 and another Th2-specific, inducible protein complex interact with the IL-4/IL-13 intergenic DNase I hypersensitive region specifically in Th2 cells.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 References
 
Coordinate regulation of IL-4, IL-13, and IL-5 determines the typical immune responses observed during infection by extracellular pathogens, helminthic parasites, and in atopic or allergic manifestations such as asthma (1, 2, 3). The genes encoding IL-4, IL-13, and IL-5 are closely linked over a 160-kb genomic region of human chromosome 5 and the syntenic region of mouse chromosome 11 (4). Of these, the IL-4 and IL-13 genes reside only 13 kb apart. Given the proximity of the IL-4, IL-13, and IL-5 genes as well as their coordinate expression after T cell activation, the expression of these Th2-specific cytokine genes could be regulated as a single transcriptional locus.

The promoter regions of IL-4 and IL-5 have been analyzed extensively and various transcription factors required for the activation of these genes have been identified (2, 3, 5, 6). However, it has now become clear that the expression level mediated by the IL-4 promoter alone is extremely weak, suggesting that optimal IL-4 gene transcription may require a distinct regulatory region outside of the promoter (7). Although most studies on the control of cytokine gene expression have focused on the proximal promoter regions, many tissue- and developmental stage-specific genes are regulated at the level of chromatin structure. Active genes are often found in regions of "decondensed" chromatin associated with acetylated histones, and are hypomethylated (8). We previously identified three DNase I hypersensitive (DH)4 sites, HSS1, HSS2, and HSS3, within the mouse IL-13/IL-4 intergenic region (9). Intriguingly, HSS1 and HSS2 are induced during Th2 development (9). Moreover, it has recently been demonstrated that the DNA segment containing HSS1 and HSS2, termed conserved noncoding sequence (CNS)-1, is highly conserved among mammals and the 1.3-kb genomic region containing CNS-1 is crucial for the expression of IL-4, IL-13, and IL-5 (10). Agarwal et al. (11, 12) also identified several Th2-specific as well as non-Th subset-specific DH sites in the flanking regions of the IL-4 and IL-13 genes.

The critical role of Stat6 in Th2 development has been shown in gene-disrupted mice (13, 14, 15). Conditional activation of Stat6 by using a Stat6-estrogen receptor (ER) fusion protein (Stat6:ER) proved that the activation of Stat6 in addition to a TCR signal is sufficient to induce Th2 differentiation (16). It has been demonstrated that Stat6 is required to induce DH sites in the flanking regions of the IL-13 and IL-4 genes (11). However, it remained to be determined whether the activation of Stat6 alone is sufficient to create an open chromatin conformation, especially at the IL-4/IL-13 intergenic region.

GATA-3 is selectively expressed in Th2 subset, and plays a crucial role in Th2 development (17, 18, 19). However, the mechanism by which GATA-3 regulates IL-4 and IL-13 gene expression remains to be clarified. Several studies have provided evidence that GATA-3 directly activates the IL-5 promoter (17, 20, 21, 22), but not the IL-4 promoter (21, 22, 23), suggesting that GATA-3 controls IL-4 expression through the regulatory region outside of the promoter or by a mechanism other than transactivation, such as chromatin remodeling. We have recently demonstrated that ectopic expression of GATA-3 results in the induction of Th2-specific DH site within the second intron of the IL-4 gene in a fully differentiated Th1 clone (23). Ouyang et al. (24) recently showed that, in developing Th2 cells, overexpression of GATA-3 leads to the induction of Th2-specific DH sites in the flanking region of the IL-4 gene even in a Stat6-deficient background. However, the role for GATA-3 in the chromatin remodeling at the flanking region of the IL-13 gene has not been addressed. Moreover, as for the IL-4/IL-13 intergenic region, the molecular mechanism underlying Th2-specific chromatin remodeling remains unknown. It would be important to determine whether a single factor is responsible for the induction of an extended open chromatin conformation over the entire IL-4/IL-13 locus.

In this study, we demonstrate that the ectopic activation of either Stat6 or GATA-3 during Th cell differentiation induces chromatin remodeling not only at the flanking regions of the IL-4 and IL-13 genes but also at the IL-4/IL-13 intergenic region, which directly overlaps with the coordinate regulatory region for the clustered Th2-specific cytokine genes. We also show, for the first time, that GATA-3 associates with HSS2-spanning region specifically in Th2 cells. Furthermore, we identified Th2-specific protein complex that interacts with HSS1 in T cell activation-dependent manner.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 References
 
Cytokines and Abs

Recombinant mouse IL-2, IL-4, IL-12, and purified rat anti-mouse IL-4 Ab (11B11) were purchased from R&D Systems (Minneapolis, MN).

Retroviral transduction

Purification by cell sorting and primary stimulation of naive Th cells from DO11.10 TCR{alpha}ß-transgenic mice (25) was performed as previously described (9). Retroviral constructs pMX-ER, pMX-Stat6:ER, and pMXI-GATA-3-EGFP and the protocol for preparation of retrovirus were described previously (16, 19, 23). On days 1 and 2 after primary antigenic stimulation under Th1-polarizing conditions, cells were infected with retrovirus-containing supernatants in the presence of 0.5 µg/ml polybrene (Sigma, St. Louis, MO). Cells infected with Stat6:ER- or ER-encoding retrovirus were thereafter cultured in the presence of 1 µM 4-hydroxytamoxifen (4-HT; Research Biochemicals, Natick, MA). On day 7, cells were sorted on the basis of enhanced green fluorescent protein (EGFP) expression. Cells were allowed to develop with weekly antigenic stimulation for another 2 consecutive weeks.

DNase I hypersensitivity analysis

Nuclei were isolated from cells (2 x 107) stimulated with PMA and A23187 as previously described (9). Varying amounts of DNase I (Worthington Biochemical, Lakewood, NJ) were added to aliquots of nuclei (1 x 108/ml), which were then incubated at 37°C for 12.5 min. Purification of genomic DNA, Southern blotting, and hybridization were conducted as described (9).

EMSA

Nuclear extracts were prepared from unstimulated or stimulated in vitro-differentiated Th1 and Th2 cells, as previously described (20). The sequence of the synthetic oligonucleotides used as probes are given in Fig. 2Goa. In the competition experiments, the following oligonucleotides were used (only the sense strands are shown): AP-1 5'-CGCTTGATGACTCAGCCGGAA-3'; T{alpha}GATA 5'-GTTAGAGATAGCATCGCCCCA-3'.



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FIGURE 2. a, The nucleotide sequences of CNS-1 (GenBank accession number AC005742: 99820–100225). Lines above and below the sequences represent possible binding sites for transcription factors. The nucleotide sequences of the sets of oligonucleotides used in EMSA are shown. bd, EMSA was performed by using in vitro-differentiated DO11.10 Th1 and Th2 nuclear extracts and 32P-labeled oligonucleotides in the absence (-) or presence of excess amounts of indicated unlabeled oligonucleotides or Ab.

 

    Results and Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 References
 
Stat6 and GATA-3 induce an accessible chromatin configuration at the IL-4/IL-13 intergenic region

We examined the functional contribution of Stat6 in the Th2-specific remodeling of the IL-4/IL-13 intergenic region. Although Stat6 is expressed in both Th1 and Th2 cells, its phosphorylation and activation occur exclusively in Th2 cells (26). Thus, we used Stat6:ER, a fusion protein of Stat6 and the modified hormone-binding domain of the ER (16). It is activated by estrogen analogues such as 4-HT, allowing us to analyze the Stat6-specific effects independently of IL-4 stimulation (16, 27). We introduced retroviral vectors encoding Stat6:ER bicistronically with EGFP (pMX-Stat6:ER) or the control ER construct (pMX-ER) into naive Th cells of DO11.10 TCR{alpha}ß-transgenic mice and let them develop under Th1-polarizing conditions in the presence of 4-HT. On day 7, EGFP+ cells were purified by cell sorting and allowed to develop with weekly antigenic stimulation for another 2 consecutive weeks, after which the chromatin structure of the IL-4/IL-13 locus was analyzed. As shown previously (16), introduction of pMX-Stat6:ER, but not pMX-ER, resulted in the induction of IL-4 production as well as a reduction in IFN-{gamma} production (data not shown).

In RV-Stat6:ER-infected cells, Th2-specific DH sites HSS1 and HSS2 (9) were induced in the IL-4/IL-13 intergenic region (Fig. 1Goa). In these cells, all the previously identified Th2-specific DH sites in the flanking regions of the IL-13 and IL-4 genes (11) were observed as well (Fig. 1Goa). Additionally, two novel DH sites, both of which we designated II', were identified within the second and first intron of the IL-4 and IL-13 genes, respectively (Fig. 1Goa). The same DH sites were also detected in a Th2 clone (D10), but not in a Th1 clone (HDK1) or in in vitro-differentiated Th1 cells (data not shown). In contrast, none of the Th2-specific DH sites were observed in RV-ER-infected cells; only those that have been shown to exist in both Th subsets were observed (Fig. 1Goa). These results indicate that the activation of Stat6 during Th cell differentiation is sufficient for the induction of an accessible chromatin configuration at the IL-4/IL-13 intergenic region as well as at the flanking regions of the IL-4 and IL-13 genes.



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FIGURE 1. DNase I hypersensitivity of Th cells infected with RV-Stat6:ER, RV-ER (a), or R-GATA-3-EGFP (b), and developed under Th1-polarizing conditions. Asterisks indicate the positions of the parental fragment. Sizes of the DNA fragments in kb are indicated on the left. c, Locations of the DH sites and CNS-1 are indicated by arrows and the shaded bar, respectively. HSS1 and HSS2 are located 1.6 and 1.8 kb upstream of the ScaI site.

 
We have recently shown that GATA-3 is one of the downstream targets of Stat6 (16). To examine possible involvement of GATA-3 in remodeling of the IL-4/IL-13 intergenic region, we infected naive Th cells of DO11.10 TCR{alpha}ß-transgenic mice with a GATA-3-encoding retrovirus (R-GATA-3-EGFP) and let them develop under Th1-polarizing conditions. An open chromatin conformation was induced in the IL-4/IL-13 intergenic region, as evidenced by the appearance of the Th2-specific DH sites, HSS1 and HSS2 (Fig. 1Gob). Th2-specific DH sites were also induced in the flanking regions of the IL-4 and IL-13 genes (Fig. 1Gob). Taken together, we propose that the induction of Th2-specific chromatin remodeling of the entire IL-4/IL-13 locus is mediated through GATA-3, which functions downstream of Stat6. We cannot rule out the possibility that the three sets of DH sites, one in the IL-4 locus, another in the IL-4/IL-13 intergenic region, and third in the IL-13 locus, are independently regulated and are induced in distinct subpopulations of cells. Although currently no reliable experimental technique is available to analyze DH sites at a single-cell level, it would be important to address this issue in future by clonal or single cell studies.

Th2-specific factors interact with the region spanning HSS1 and HSS2

It recently has been demonstrated that the DNA segment containing HSS1 and HSS2, termed CNS-1, is highly conserved among mammals and the 1.3-kb genomic region containing CNS-1 is crucial for the expression of the IL-4, IL-13, and IL-5 genes (10). Detection and analysis of molecules that associate with HSS1 and HSS2 should facilitate further elucidation of the molecular events occurring in Th2-specific, coordinate expression of these Th2 cytokine genes.

Inspection of CNS-1 by the aid of a computer data base (MatInspector V2.2; http://transfac.gbf-braunschweig.de/cgi-bin/matSearch/matsearch.pl) identified several transcription factor binding motifs including those for NFAT, c-Myb, AP-1, activating transcription factor, cAMP response element binding protein, and Ikaros (Fig. 2Goa, GenBank accession numbers AC005742: 99820–100225). Interestingly, a potential binding site for GATA-3 was identified at the 5' end of CNS-1, which perfectly overlaps with the HSS2 (Figs. 1Goc and 2a). Although several GATA-3 binding sites have been reported in the IL-4/IL-13 locus (12, 22), binding of GATA-3 to CNS-1 has not been addressed. Thus, we performed EMSA using in vitro-differentiated DO11.10 Th1 and Th2 nuclear extracts. Using oligonucleotide probe IIa, a DNA-protein complex that we designated HSS2-I was formed with Th2 but not with Th1 nuclear extracts (Fig. 2Go, a and b). Intensity of the band containing HSS2-I increased after T cell activation (Fig. 2Gob). The formation of HSS2-I was abrogated by introducing a substitution mutation into WGATAR motif (data not shown), or by adding excess amounts of an oligonucleotide containing a GATA-3 binding site from the human TCR{alpha} gene enhancer (T{alpha}GATA) (Fig. 2Gob). Conversely, IIa, but not the mutated IIa oligonucleotide inhibited the binding of GATA-3 to the T{alpha}GATA oligonucleotide (Fig. 2Gob). Moreover, pretreatment with anti-GATA-3 Ab supershifted HSS2-I (Fig. 2Gob). These results indicate that HSS2-I contains GATA-3.

As for HSS1-spanning region, potential binding sites for known Th2-specific transcription factors such as Stat6, GATA-3, or c-Maf were not detected (Fig. 2Goa). To investigate the NFs interacting with HSS1, we performed EMSA using sets of overlapping oligonucleotide probes spanning HSS1 (Fig. 2Goa, Ia-Ig). Several constitutive as well as inducible complexes were identified using Th1 and Th2 nuclear extracts (Fig. 2Goc). Interestingly, when oligonucleotides If and Ig were used as probes, T cell activation-inducible complexes were detected specifically in Th2 nuclear extracts (Fig. 2Goc). Cross competition assays with either oligonucleotide revealed that the binding proteins recognize the same DNA sequence within these overlapping probes (Fig. 2God). We designated these complexes HSS1-I. The inducibility of HSS1-I correlates with the enhanced accessibility of HSS1 upon T cell activation (9). The overlapping portion of probes If and Ig contained the DNA sequence closely resembling the consensus AP-1 binding site (Fig. 2Goa). The formation of HSS1-I was efficiently inhibited by adding excess amounts of an oligonucleotide containing the consensus AP-1 binding site, but not by the Ig oligonucleotide with a substitution mutation in the putative AP-1 binding motif (Fig. 2God). These results suggest that HSS1-I may include DNA binding proteins identical or closely related to AP-1. The Fos/Jun heterodimer has been shown to disrupt the nucleosome structure and to facilitate the binding of a second transcription factor in vitro (28), suggesting the potential involvement of HSS1-I in alteration of the chromatin structure. Because each component of the AP-1 family proteins has been detected in both Th1 and Th2 nuclear extracts (29), HSS1-I may contain additional Th2-specific NF(s). It has been demonstrated that c-Maf can activate the IL-4 promoter synergistically with Jun B (30). However, the nucleotide sequence surrounding the putative AP-1 site in the probe does not match the consensus binding site for c-Maf (Fig. 2Goa) and anti-c-Maf Ab failed to supershift HSS1-I (data not shown).

Recently, it has been shown that following T cell activation, a Th2-specific, cyclosporin A-sensitive DH site designated VA is induced at 3' of the IL-4 gene (12). Interestingly, canonical GATA sites reside in the region surrounding VA, and GATA-3 binds in vivo to the genomic region spanning VA (12). As for the IL-4/IL-13 intergenic regulatory region, our results indicate possible binding of GATA-3 to the DNA segment encompassing Th2-specific DH site, HSS2 (Fig. 2Gob). It would thus appear that GATA-3 induces chromatin remodeling through direct association with Th2-specific DH sites scattered over the entire IL-4/IL-13 locus. Consistent with this notion, GATA-1, another member of the GATA family of proteins, has been shown to play an essential role in the induction of the erythroid-specific DH site of the human ß-globin locus control region and in the chicken ßA/{epsilon}-globin gene through direct association with its recognition sites (31, 32). We have recently shown that a GATA-3 mutant lacking its N-terminal finger, and thus unable to bind to its recognition sequence, is still capable of redirecting the Th1-differentiated phenotype of a Th1 clone into IL-4 expressing cells (23). Therefore, GATA-3 might regulate the chromatin structure of the IL-4/IL-13 locus in the absence of direct DNA binding as well, presumably through recruiting chromatin remodeling complexes. It is also possible that GATA-3 up-regulates Th2-specific cytokine transcription from the "opened" HSS2 in fully differentiated effector Th2 cells. In either case, it would be important to determine whether GATA-3 interacts with the chromatin of the HSS2 region in vivo.

In conclusion, our results revealed that GATA-3 induces the chromatin remodeling at the IL-4/IL-13 intergenic regulatory region, and Th2-specific protein complexes containing GATA-3 associate with this region. Based on these findings, we propose that establishment of an accessible chromatin conformation at the IL-4/IL-13 intergenic regulatory region by GATA-3 may underlie the coordinate expression of the clustered Th2-specific cytokine genes.


    Acknowledgments
 
We thank S. Namiki for technical assistance, A. Kaneko for help in cell sorting, and K. Conger for critical reading of the manuscript.


    Footnotes
 
1 N.T. is a Research Fellow of the Japan Society for the Promotion of Science. Back

2 Current address: Howard Hughes Medical Institute, University of Chicago, 5841 South Maryland Avenue, MC1028, Chicago, IL 60637. Back

3 Address correspondence and reprint requests to Dr. Shoichiro Miyatake, Department of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Back

4 Abbreviations used in this paper: DH, DNase I hypersensitive; CNS, conserved noncoding sequence; EGFP, enhanced green fluorescent protein; ER, estrogen receptor; 4-HT, 4-hydroxytamoxifen Back

Received for publication September 13, 2000. Accepted for publication October 16, 2000.


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 Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 References
 

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