Article


Nature Immunology 10, 872 - 879 (2009)
Published online: 28 June 2009 | Corrected online: 5 July 2009 | doi:10.1038/ni.1747

Mina, an Il4 repressor, controls T helper type 2 bias

Mariko Okamoto1,5, Melanie Van Stry2,5, Linda Chung2, Madoka Koyanagi2, Xizhang Sun3, Yoshie Suzuki1, Osamu Ohara4, Hiroshi Kitamura4, Atsushi Hijikata4, Masato Kubo1 & Mark Bix2


T helper type 2 (TH2) bias, which is the propensity of naive CD4+ T cells to differentiate into interleukin 4 (IL-4)-secreting TH2 cells, is a genetic trait that affects susceptibility to infectious, autoimmune and allergic diseases. TH2 bias correlates with the amount of IL-4 initially secreted by newly activated helper T cells that feeds back positively through the pathway of the IL-4 receptor and the transcription factors STAT6 and GATA-3 to drive TH2 development. Here we identify Mina, a member of the jumonji C (JmjC) protein family, as a genetic determinant of TH2 bias. Mina specifically bound to and repressed the Il4 promoter. Mina overexpression in transgenic mice impaired Il4 expression, whereas its knockdown in primary CD4+ T cells led to Il4 derepression. Our findings collectively provide mechanistic insight into an Il4-regulatory pathway that controls helper T cell differentiation and genetic variation in TH2 bias.


Naive CD4+ T cells are multipotent sentinels of the immune system, poised to respond to instructive signals from antigen-presenting cells by differentiating into distinct effector cell lineages. These include T helper type 1 (TH1) and TH2 cells, which are adapted differently for the control of intracellular and extracellular pathogens, respectively, in part through developmentally acquired potential for high expression of distinct cytokine genes1. Dysregulated CD4+ T cell development can promote susceptibility to infectious, autoimmune and allergic diseases2, 3, 4, 5, 6, 7, 8, 9.

Interleukin 4 (IL-4; A001262), the canonical TH2 effector cytokine, is also a critical developmental determinant that promotes TH2 differentiation and inhibits TH1 differentiation10. Recently activated helper T cells make small but functional amounts of IL-4 that induce positive feedback through the IL-4 receptor (A001263) and the transcription factors STAT6 (A002236) and GATA-3 (refs. 11,12) to promote the differentiation of TH2 cells able to secrete copious amounts of IL-4 (refs. 10,13,14,15,16,17,18). Thus, regulation of autocrine IL-4 expression by activated helper T cells is a key control point in T helper cell lineage commitment. Nonetheless, the molecular mechanism underlying this regulation is incompletely understood.

TH2 bias is a complex genetic trait characterized by variation in the propensity of naive helper T cells to differentiate into TH2 (rather than TH1) cells. TH2 bias, measured experimentally as the amount of IL-4 produced by effector CD4+ T cells differentiated in vitro from naive helper T cells activated in 'neutral' conditions (that is, activated without the addition of exogenous cytokines, except IL-2, and cultured without cytokine-specific antibodies), varies over 50-fold from the high-producer phenotype of BALB/c mice to the low-producer phenotype of B10.D2 mice and correlates with susceptibility to TH2-dependent diseases such as bronchial asthma and leishmaniasis14, 15, 16, 19, 20, 21, 22. Various cellular mechanisms have been suggested as the basis for TH2 bias, including variation in the sensitivity to prostaglandin E2–dependent inhibition of interferon-gamma production23, the timing of IL-12 receptor-beta2 downregulation24, 25 and the capacity of activated helper T cells to produce autocrine IL-4 (refs. 14,15,16,20). Genetic approaches to delineate TH2 bias have yielded many quantitative trait loci spread across mouse chromosomes 5, 12, 14 15, 16, 17, 18 and 19 (refs. 14,26,27,28,29) and a single discrete genetic locus on chromosome 11 (refs. 24,25). Several quantitative trait loci have been confirmed and isolated as discrete genetic loci by interval-specific congenic mapping14, 26, 28. However, so far none of the underlying genetic determinants have been identified.

Here we combine classical genetic and transcriptional profiling analyses to identify Mina, a member of the jumonji C (JmjC) protein family, as a determinant of the TH2 bias–regulatory locus Dice1b (called 'Dice1.2' here), which was identified by its activity in the autocrine IL-4 pathway of activated helper T cells28. We found that TH2 bias and autocrine Il4 expression correlated inversely with the Mina transcriptional rate, which in turn correlated with a Mina locus haplotype. Consistent with those findings, Mina bound to the Il4 promoter, where it repressed Il4 expression. We propose that a regulatory polymorphism that controls Mina expression in activated helper T cells determines the strength of Mina-dependent Il4 repression and hence the degree of autocrine IL-4 production and, ultimately, the extent of TH2 differentiation, thereby accounting at least in part for strain-specific differences in TH2 bias.

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Results

Mina is a Dice1.2 candidate gene

Through the use of quantitative trait loci and interval-specific congenic mapping, an Il4-regulatory locus controlling TH2 bias, Dice1.2, has been mapped to a 26.8-megabase (Mb) genomic interval in chromosome 16 (refs. 14,28; Fig. 1a). To resolve that interval further, we generated the subcongenic strain C16D2/8D, in which the Dice1.2-spanning genomic segment derived from B10.D2 mice (low TH2 bias) that is present in the congenic strain C16D2/8 on the BALB/c background (high TH2 bias)28 is bisected to 14.1 Mb (D16MIT138–MB04; Fig. 1a). We primed splenic CD4+ T cells from BALB/c, B10.D2 and C16D2/8D mice for 16 h before analyzing Il4 expression by quantitative RT-PCR. As expected, control BALB/c and B10.D2 cells showed phenotypes of high and low TH2 bias, respectively (Fig. 1b). The production of Il4 transcripts by C16D2/8D cells was similar to that of B10.D2 cells and was significantly less than that of BALB/c cells (P = 0.0317). This result indicates that Dice1.2 is in the 14.1-Mb C16D2/8D congenic interval that spans from D16MIT138 to MB04 and contains 121 predicted or known genes30. As 29 of these encode olfactory receptors, 92 remained as Dice1.2 candidates.

Figure 1: Mina is a Dice1.2 candidate gene.

Figure 1 : Mina is a Dice1.2 candidate gene.

(a) Location of congenic intervals in chromosome 16 of the C16D2/8 (–) and C16D2/8D (D) mouse strains, showing the chromosomal regions inherited from the B10.D2 strain (gray), the BALB/c strain (white) or ambiguous (striped); cyan dots indicate genotyped locations. Right margin, genotyping markers (red, Mina). Left margin, original (26.8 Mb) and newly identified (14.1 Mb) Dice1.2 genetic intervals, respectively. (b) Il4 expression in TCR crosslinking–activated CD4+ T cells from BALB/c, B10.D2 and C16D2/8D mice (n = 2–5 per strain; results are presented in arbitrary units relative to the expression of Hprt1 (encoding hypoxanthine guanine phosphoribosyl transferase). Each symbol represents an individual mouse; small horizontal lines indicate the mean. *P = 0.0317 (t-test). Data are representative of two experiments with similar results.

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The polymorphisms in Dice1.2 that underlie the genetic variability in TH2 bias may reside in coding or regulatory sequence. To test for the latter possibility, we investigated genes in the Dice1.2 interval by transcriptional profiling with mRNA isolated from BALB/c and C16D2/8D CD4+ T cells stimulated by T cell antigen receptor (TCR) crosslinking for 16 h, a time at which differences in Il4 expression were nearly maximal. The Affymetrix gene chip we used for initial screening contained 30 Dice1.2 candidate genes. Of these, half were undetectable, and of the remainder, all but one had similar expression in BALB/c and C16D2/8D cells. The one exception was Mina, whose expression was two- to threefold higher in C16D2/8D cells than in BALB/c cells (Supplementary Fig. 1). Although expression profile analysis of the remaining genes in the Dice1.2 interval might identify additional Dice1.2 candidates, we explored here the possibility that Mina acts as a negative regulator of Il4 expression and TH2 bias.

Inverse correlation of IL-4 and Mina

First, to investigate whether the inverse correlation in the expression of Mina and Il4 in BALB/c and B10.D2 cells could be generalized, we used quantitative RT-PCR to explore their expression in recently activated CD4+ T cells isolated from a panel of independent inbred mouse strains representing phenotypes of high and low TH2 bias. Whereas the kinetics of the transcriptional induction of Mina and Il4 was similar across the strains tested, peak magnitudes were very dissimilar and segregated the strains into two discrete groups (Fig. 2a). In the C57BL/6, B10.D2 and C3H/HeN strains, which have low TH2 bias, high Mina expression correlated with low Il4 expression, whereas in the BALB/c, DBA/1J, DBA/2J and DBA/2N strains, which have high TH2 bias, the converse was true (Fig. 2a). Thus, the inverse correlation in Il4 and Mina expression could be generalized across strains with varying phenotypes of TH2 bias.

Figure 2: Inverse correlation of Mina and Il4 expression in naive helper T cells.

Figure 2 : Inverse correlation of Mina and Il4 expression in naive helper T cells.

(a) Time course of the expression of Mina mRNA (left) and Il4 mRNA (right) in TCR crosslinking–activated CD4+ T cells isolated from strains with low TH2 bias (B10.D2, C57BL/6 and C3H/HeN; filled symbols) and high TH2 bias (BALB/c, DBA/1J, DBA/2J and DBA/2N; open symbols); results are presented in arbitrary units relative to the expression of Actb (encoding beta-actin). Data are from three independent experiments (mean and s.e.m.). (b) Time course of the expression of Mina, Il4 and Ifng mRNA in BALB/c or C57BL/6 naive helper T cells activated by TCR crosslinking (top row) or from TH1- or TH2-primed C57BL/6 naive helper T cells (bottom); results are presented in arbitrary units relative to Hprt1 expression. Data are representative of two independent experiments (error bars, s.e.m. of triplicate PCR). (c) Mina expression in CD4+ T cells stimulated for 24 h with TCR crosslinking in the presence of 'graded' doses of IL-4 (B10.D2) or anti-IL-4 (BALB/c); results are presented in arbitrary units relative to Actb expression. Data are from three independent experiments (mean and s.e.m.). (d) Mina expression in B10.D2 CD4+ T cells stimulated for 24 h in the presence of anti-IL-12; results are presented (in arbitrary units) relative to Actb expression. Data are from three independent experiments (mean and s.e.m.).

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From the analysis reported above of splenic T cell samples enriched for CD4+ cells, it was not clear whether the inverse correlation in the expression of Il4 and Mina occurred in naive progenitor helper T cells or effector helper T cells. To investigate this question, we compared the expression of genes encoding cytokines in highly purified naive helper T cells from BALB/c and C57BL/6 mice. Quantitative RT-PCR analysis of naive helper T cells (99% CD4+CD62LhiCD44lo; less than 0.2% contamination by natural killer T cells) stimulated for 24 h with plate-bound antibody to TCR (anti-TCR) and anti-CD28 demonstrated an inverse correlation in the expression of Mina and Il4, similar to that in the cell samples enriched for CD4+ cells (Fig. 2b, top). Next we compared restimulated memory effector cells generated from C57BL/6 helper T cells primed in TH1 and TH2 conditions. As expected, Il4 expression was low and high in TH1- and TH2-primed cells, respectively (Fig. 2b, bottom). However, in contrast to naive helper T cells from C57BL/6 and BALB/c mice, TH1 and TH2 cells had similar kinetics and magnitude of Mina expression. Thus, the disparate Il4 expression potential of TH1 and TH2 cells is not inversely correlated with Mina expression. In contrast, natural variation in the capacity of naive helper T cells to express Il4 is inversely correlated with Mina expression.

Mina acts 'upstream' of IL-4 and IL-12

Two possibilities could account for the inverse correlation in the expression of Il4 and Mina: negative regulation of Il4 by Mina, or negative regulation of Mina by IL-4 signaling. To distinguish between these possibilities, we assessed the abundance of Mina mRNA in activated B10.D2 CD4+ T cells in the presence and absence of exogenously added IL-4. The addition of IL-4 to B10.D2 CD4+ T cells did not diminish its 'high-Mina' phenotype. Conversely, IL-4 neutralization with an IL-4-specific antibody did not enhance the 'low-Mina' phenotype of BALB/c CD4+ T cells (Fig. 2c). We obtained similar results with highly purified naive helper T cells (Supplementary Fig. 2a). Given the ability of IL-12 to promote and inhibit TH1 development and TH2 development, respectively, it was also possible that Mina expression was regulated by IL-12. However, neutralization of IL-12 with an IL-12-specific antibody did not diminish the high Mina expression of B10.D2 cells (Fig. 2d). Furthermore, the addition of IL-12 did not enhance the low Mina expression of BALB/c naive helper T cells (Supplementary Fig. 2b). Together these results indicate that neither the IL-4 signaling pathway nor the IL-12 signaling pathway regulates Mina expression, which provides support for the idea that Mina acts as a negative regulator of Il4 expression in naive helper T cells.

Mina is transcriptionally regulated

We next sought to determine whether differences in Mina transcript abundance led to differences in Mina protein abundance. We activated purified BALB/c and C57BL/6 naive helper T cells over a 72-hour time course with plate-bound anti-TCR and anti-CD28 and analyzed the resulting nuclear and cytoplasmic extracts by immunoblot with a Mina-specific antibody (Fig. 3a). Whereas cytosolic Mina increased with time, nuclear Mina appeared transiently, peaking around 24 h in both BALB/c cells and C57BL/6 cells. In both subcellular compartments, Mina protein amounts were consistently higher (about two- to fivefold) in C57BL/6 cells than in BALB/c cells, which demonstrated tight linkage between the abundance of Mina protein and that of Mina mRNA. To determine whether Mina was regulated transcriptionally, we exploited the fact that the abundance of pre-mRNA correlates with transcriptional rate31. Measurement of Mina pre-mRNA abundance showed higher expression in newly activated C57BL/6 helper T cells than in newly activated BALB/c helper T cells, which correlated with the differences in Mina mRNA abundance (Fig. 3b). These results collectively indicate that Mina protein abundance is transcriptionally regulated.

Figure 3: Mina is transcriptionally regulated.

Figure 3 : Mina is transcriptionally regulated.

(a) Immunoblot analysis of Mina and actin in cytosolic and nuclear extracts of BALB/c and C57BL/6 naive helper T cells activated for various times (above lanes) with phorbol 12-myristate 13-acetate (PMA) and ionomycin. The top band in the nuclear Mina immunoblot is nonspecific. Right, quantification of Mina expression, presented relative to actin expression. Data are representative of two independent experiments. (b) Time course of the expression of Mina pre-mRNA in naive helper T cells isolated from pools of BALB/c mice (n = 5) and C57BL/6 mice (n = 20) and activated by TCR crosslinking, measured by quantitative PCR with primers targeting sequences from Mina intron 1 and presented (in arbitrary units) relative to Hprt1 expression. Data are representative of two independent experiments (error bars, s.e.m. of triplicate PCR).

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To explore whether regulatory polymorphisms could account for the differences in Mina transcription in strains with high and low TH2 bias, we sequenced the 5' end of the Mina genomic locus (including intron 1 and 1,304 base pairs (bp) of the promoter) from strains with high TH2 bias (BALB/c and DBA/2J) and those with low TH2 bias (C57BL/6, B10.D2/OsnJ and C3H/HeN). We identified 21 single-nucleotide polymorphisms (SNPs) that precisely defined two haplotypes (Fig. 4) that correlated with the phenotypes of TH2 bias and Mina expression (Fig. 2). Thus, Mina haplotypes are a useful genetic marker for TH2 bias and may contain regulatory polymorphisms responsible for differences in Mina expression across strains with distinct phenotypes of TH2 bias.

Figure 4: Mina haplotype can be used to predict TH2-bias phenotype.

Figure 4 : Mina haplotype can be used to predict TH2-bias phenotype.

(a) Promoter-proximal end of the Mina genomic locus, showing the 21 SNPs identified across this interval, along with exons (red), the coding region (yellow) and conserved noncoding sequences (CNS1–CNS6; cyan). (b) Position (relative to the translational start site in exon 2) and allelic identity of each SNP for three strains with low TH2 bias (red) and two strains with high TH2 bias (green; - indicates a gap in the sequence).

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Mina specifically binds and represses the Il4 promoter

To investigate whether Mina can repress transcription from the Il4 promoter, we did transient reporter assays, cotransfecting 68-41 mouse T cell hybridoma cells with a Mina or empty expression vector and a luciferase reporter driven by either an Il4 promoter or an Il2 promoter32. Mina inhibited luciferase activity driven by the Il4 promoter but not activity driven by the Il2 promoter (Fig. 5a). To define the Mina-responsive region in the 766-bp Il4 promoter, we used the transient reporter assay to study a series of Il4 promoter deletion mutants. Neither truncation of the Il4 promoter to 300 bp nor truncation to 140 bp was sufficient to eliminate sensitivity to Mina-dependent repression (Fig. 5a). Thus, a target site for the repressive activity of Mina is in the first 140 bp of the Il4 promoter.

Figure 5: Mina can bind to and repress transcription from the Il4 promoter.

Figure 5 : Mina can bind to and repress transcription from the Il4 promoter.

(a) Transcriptional response of the Il4 promoter (left) and Il2 promoter (right) to Mina, assessed in cells transduced with a Mina or empty (-) expression vector and a luciferase reporter driven by the Il4 promoter (promoter deletion mutant length below (in bp): 766, positions -830 to -64; 300, positions -364 to -64; 140, positions -204 to -64 (all positions relative to the translational start site)) or Il2 promoter and then left unstimulated (TCR–) or stimulated for 12 h with anti-TCR (TCR+). *P < 0.05 (t-test). Data are from three independent experiments (average and s.e.m.). (b) Nucleotide sequence of the proximal Il4 promoter, showing regions used as oligonucleotide probes (A, B, C and D; underlined) in EMSA. (c) EMSA of nuclear extracts of B10.D2 CD4+ T cells stimulated for 24 h by TCR crosslinking and incubated with end-labeled probes A–D in the presence (right; probes A and B only) or absence (left) of 2 mug anti-Mina. Arrows indicate the location of the nucleoprotein complex containing Mina. Data are representative of three independent experiments. (d) ChIP analysis of chromatin-bound Mina at five sites along the Il4 promoter (horizontal axis; positions relative to translational start site) and at the locus encoding CD3epsilon (negative control) in BALB/c and B10.D2 CD4+ T cells stimulated for 24 h by TCR crosslinking; results are presented as immunoprecipitated relative to input. *P < 0.05 (t-test). Data are from five independent experiments (mean and s.e.m.).

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To further refine the Mina responsive region, we used electrophoretic mobility-shift assay (EMSA). We tested nuclear extracts isolated from TCR-stimulated B10.D2 CD4+ T cells against a series of end-labeled DNA probes spanning the first 140 bp of the Il4 promoter (Fig. 5b). Nucleoprotein complexes were formed with probe A (positions -188 to -158) and probe B (positions -157 to -128) but not probe C (positions -127 to -98) or probe D (positions -97 to -69; Fig. 5c); however, only the probe B complex was sensitive to disruption by a Mina-specific antibody. Thus, Mina can associate with the Il4 promoter over the 30-bp region of probe B that extends from position -157 to position -128.

To determine whether Mina binds to the Il4 promoter in vivo, we used anti-Mina for chromatin immunoprecipitation (ChIP) analysis of BALB/c and B10.D2 CD4+ T cells that had been activated for 24 h. Consistent with the binding activity detected by EMSA in the region from position -157 to position -128, we found Mina enrichment in the Il4 promoter but not in the promoter of the gene encoding CD3epsilon (Fig. 5d). Furthermore, the magnitude of binding activity at the Il4 promoter was consistently higher in B10.D2 cells than in BALB/c cells, which correlated with the relative expression of Mina in these two strains (Fig. 2e). A broad ChIP survey of the entire TH2 locus in B10.D2 CD4+ T cells activated for 24 h also detected a strong peak of Mina binding at the Il4 promoter (Supplementary Fig. 3). These data collectively support a model in which Mina is recruited to the proximal Il4 promoter, where it exerts a concentration-dependent transcription-repressive effect.

Recruitment of Mina to the Il4 promoter requires NFAT

As Mina lacks a predicted DNA-binding domain, it is likely that its recruitment to the Il4 promoter is indirect. Probe B contains published binding sites for the transcription factors NFAT (NFATc1 (A001640) and NFATc2 (A000024)) and Oct33, 34, which raises the possibility of their involvement in recruiting Mina to the Il4 promoter (Fig. 6a). To test this possibility, we used wild-type probe B and a mutant probe B (BNM) unable to bind NFAT34 for EMSA with nuclear extracts from the T cell thymoma line EL4, which expresses Mina35. Nuclear extracts from activated but not resting EL4 cells (and C57BL/6 CD4+ T cells) formed a nucleoprotein complex with wild-type probe B (Supplementary Fig. 4). This complex was sensitive to disruption by a Mina-specific antibody (Fig. 6b), which indicated that the probe B complex formed with EL4 extracts, like that formed with B10.D2 CD4+ T cell extracts, contained Mina. Although a wild-type NFAT consensus sequence was able to compete with probe B for complex formation, a wild-type Oct consensus sequence did not (data not shown), which suggests that the Mina complex contains NFAT but not Oct. Furthermore, a probe B mutant unable to bind Oct was still able to form the Mina complex (data not shown). Thus, Oct is neither a constituent of the Mina–probe B complex nor required for recruitment of Mina to the Il4 promoter.

Figure 6: Recruitment of Mina to the Il4 promoter requires NFAT.

Figure 6 : Recruitment of Mina to the Il4 promoter requires NFAT.

(a) Oligonucleotide probes from the Il4 promoter (B and BNM) and Il2 promoter (IL-2) used in the EMSA and DNA-precipitation experiments in b,c; above, NFAT- and Oct-binding sites. Probe BNM is identical to probe B except for a dinucleotide mutation in the NFAT-binding site (bold italics). (b) EMSA of nuclear extracts of EL4 cells induced for 4 h with PMA-ionomycin and incubated with end-labeled probe B (*B) or probe BNM (*BNM) in the presence or absence of 100, 33 or 11 ng (wedges) of unlabeled probe B or probe BNM (left) or with end-labeled probe B and 3 mug anti-Mina, 2 mug anti-NFATc1, 2 mug anti-NFATc2 or rabbit serum (right). NE–, absence of nuclear extract; NE+, presence of nuclear extract. Thick and thin arrows indicate locations of the Mina complex and the anti-NFAT 'supershifted' complex, respectively. Data are representative of three independent experiments. (c) Blots of precipitation products formed by the combination of biotin-labeled probes (IL-2, B and BNM) with nuclear extracts from EL4 cells induced for 4 h with PMA and ionomycin (Input), followed by isolation of complexes of DNA and protein (NFATc2 and Mina) with streptavidin-agarose beads. Data are representative of two independent experiments.

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The formation of higher-order complexes with anti-NFATc1 and anti-NFATc2 confirmed the presence of both NFAT proteins in the probe B–Mina complex (Fig. 6b and data not shown). The mutant probe BNM that is unable to bind NFAT34 did not form the Mina complex and failed to compete with probe B for complex formation (Fig. 6b), which suggests a requirement for NFAT in Mina recruitment. To confirm that idea, we did DNA precipitation assays with biotinylated probes B and BNM. Whereas both Mina and NFAT (NFATc1 and NFATc2) could be precipitated together with the biotinylated wild-type probe B, probe BNM failed to precipitate together with either NFAT protein or Mina (Fig. 6c and data not shown). Notably, a biotinylated NFAT-binding sequence from the Il2 promoter failed to precipitate Mina despite binding both NFATc1 and NFATc2 (Fig. 6c and data not shown), which indicated that NFATc1 and NFATc2 were insufficient for Mina recruitment. Finally, nuclear extracts of cells treated with the calcineurin inhibitor cyclosporin A, to prevent NFAT dephosphorylation and nuclear translocation, failed to form the Mina nucleoprotein complex (Supplementary Fig. 4). These data collectively suggest that NFAT is necessary but not sufficient for recruitment of Mina to the Il4 promoter–specific nucleoprotein complex.

Mina is necessary and sufficient to constrain IL-4 expression

To directly test whether Mina can repress Il4 transcription in CD4+ T cells, we generated three independent BDF1 times C57BL/6 mouse lines expressing a Mina transgene driven by a lymphocyte-specific proximal promoter–Emu enhancer of the gene encoding the kinase Lck36. We analyzed mice after three backcrosses to BALB/c mice, at which point they showed normal T cell development and expression of activation markers (data not shown). Using quantitative RT-PCR to compare Mina expression in CD4+ T cells, we found that all three transgenic lines had high basal Mina expression that diminished over a 48-h activation time course to lower expression similar to or higher than the peak of expression by their respective wild-type littermate controls (Fig. 7). To determine the effect of a transient enforced increase in Mina abundance on cytokine gene expression, we examined the transcriptional induction of Il2 and Il4 and of the gene encoding interferon-gamma (Ifng). Expression of Il4 was considerably impaired in all three Mina-transgenic lines relative to its expression in wild-type littermate controls, but expression of Il2 and Ifng was not (Fig. 7). Thus, a transient enforced increase in Mina in CD4+ T cells specifically impairs expression of Il4 but not of Il2 or Ifng.

Figure 7: A transient enforced increase in Mina impairs Il4 expression in CD4+ T cells.

Figure 7 : A transient enforced increase in Mina impairs Il4 expression in CD4+ T cells.

Quantitative real-time RT-PCR analysis of the expression of Mina, Il4, Il2 and Ifng in CD4+ T cells isolated from three independent lines from Mina-transgenic mice (lines 6, 38 and 21; filled symbols; n = 2 mice each) and their corresponding littermate controls (open symbols; n = 2 mice each), then stimulated for various times (horizontal axis) with anti-TCR and anti-CD28. Results are presented in arbitrary units relative to Actb expression; each line represents an individual mouse. Data are from two independent experiments (Exp 1 and 2).

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To test whether Mina-dependent repression is required to maintain normal expression of Il4, we used antisense morpholino technology to 'knock down' Mina protein in primary CD4+ T cells. At 24 h after activation, C57BL/6 CD4+ T cells pretreated for 16 h with Mina-morpholino expressed half the amount of Mina protein expressed by cells given mock pretreatment or pretreatment with control-morpholino (Fig. 8). In contrast, cells pretreated with Mina-morpholino expressed about twofold more Il4 mRNA (but not more Ifng mRNA) than did cells given mock pretreatment or pretreatment with control-morpholino (Fig. 8). Thus, the quantitative potential of CD4+ T cells to express Il4 is normally constrained by tight Mina-dependent negative regulation.

Figure 8: Il4 expression in CD4+ T cells is constrained by Mina-dependent repression.

Figure 8 : Il4 expression in CD4+ T cells is constrained by Mina-dependent repression.

Left, immunoblot analysis of the expression of Mina and actin in total cellular extracts from CD4+ T cells (4 times 106 to 6 times 106) given 16 h of mock pretreatment or pretreatment with control morpholino (CoMO) or Mina-morpholino (MinaMO) and then activated for 24 h with plate-bound anti-TCR and anti-CD28. Middle, quantification of Mina expression in the blot at left, presented relative to actin expression. Right, expression of Il4 and Ifng in the cells at left; results are presented (in arbitrary units) relative to Hprt1 expression. Data are representative of two independent experiments (mean of duplicate PCR).

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Discussion

We have identified Mina as a genetic determinant of the Il4- and TH2 bias–regulatory locus Dice1.2. Our data suggest that Mina is a necessary and sufficient dose-dependent Il4-specific repressor in naive helper T cells that affects the magnitude of the early autocrine IL-4 burst required for the 'programming' of TH2 development. Furthermore, our results have shown how natural variation in Mina transcription (probably due to regulatory SNPs at the Mina locus) contributes to natural variation in TH2 bias.

Mina belongs to the Jmj protein family whose hallmark JmjC domain is homologous to the family of Fe(II)- and 2-oxoglutarate–dependent dioxygenase enzymes. The catalytic dioxgyenase core comprises three iron-binding residues and two 2-oxoglutarate–binding residues, of which four are conserved in Mina37. Dioxygenases can catalyze a variety of post-translational modifications on substrate proteins, including demethylation and hydroxylation. For example, JMJD6, a member of the JmjC-only subfamily (to which Mina belongs), has been shown to have histone arginine–demethylase activity38, and FIH (also a member of the JmjC-only subfamily) is an asparagine hydroxylase, responsible for inactivating the transcriptional activation domain of hypoxia-inducing factor39, 40. Despite imperfect conservation of its core catalytic residues, Mina is a functional Fe(II)–2-oxoglutarate–dependent dioxygenase enzyme (C. Schofield, personal communication). Thus, a likely hypothesis is that Mina acts as an Il4 repressor by demethylating histones at key positive regulatory elements such as the 3' DNAse I–hypersensitive site V (ref. 41), reported to be required for Notch-mediated activation of autocrine expression of IL-4 in naive helper T cells42, 43. Preliminary results suggest that abundance of histone 3 trimethylated on lysine 4 is similar at DNAse I–hypersensitivity sites HSV, HSVa, HSIV and HSS3 in naive CD4+ T cells from BALB/c mice and C57BL/6 mice, inconsistent with a histone-demethylating function for Mina. Another likely hypothesis is that Mina catalyzes post-translational changes that modulate key Il4 transcription factors. In this context, it is notable that arginine methylation augments the ability of the transcription factor NIP45 to promote Il4 transcription44. Finally, it is possible that the Il4-repressive effect of Mina may be mediated by a mechanism independent of its dioxygenase activity.

Mina, which lacks an obvious DNA-binding domain, associates with a region of the Il4 promoter that contains binding sites for NFAT and Oct. Our results have indicated that whereas Oct is excluded from the Mina complex, an NFAT-dependent interaction is required for recruitment of Mina to the Il4 promoter. However, although it is necessary, NFAT is not sufficient for recruitment of Mina to the Il4 complex, as it did not associate with an Il2 promoter fragment able to recruit both NFATc1 and NFATc2. This result indicates the existence of specificity-determining sequence elements in addition to those required for NFAT recruitment. Identification of these elements may assist in the identification of factors required along with NFAT to recruit Mina to the Il4 promoter.

Mina was first identified as a nuclear antigen of 53 kilodaltons induced by the myelocytomatosis oncogene product Myc and was found to be overexpressed and associated with poor prognosis in a variety of human cancer cells45, 46, 47, 48. Studies using ChIP and tamoxifen-inducible fusion protein Myc-ERTam have shown that Mina is a direct target of Myc in human promyelocytic leukemia and human glioblastoma cells48. Comparison of the Mina promoter sequence in strains with high or low TH2 bias failed to demonstrate polymorphism in a presumptive Myc-binding site (data not shown), which suggests that differences in Myc activity may not be responsible for the differences in Mina expression in strains with high or low TH2 bias. Furthermore, Myc expression in activated naive helper T cells is similar in strains with high or low TH2 bias, and its acute deletion does not impair Mina expression in naive helper T cells (M. Koyanagi, unpublished data). Thus, in naive helper T cells, Mina may not be a true Myc target.

There are 21 SNPs of the Mina promoter and intron 1 that define two distinct haplotypes that correlate with Mina expression phenotype. The polymorphisms that underlie the differences in Mina expression probably reside in a key regulatory element whose function is modulated by one or several of the 21 (or perhaps additional) haplotype-defining SNPs. Phylogenetic sequence conservation has been used to identify gene-regulatory elements as regions of 'conserved noncoding sequence'49. We have identified six conserved noncoding sequences in the 5-kilobase region of the Mina locus containing the 21 SNPs. Four of the twenty-one haplotype-defining SNPs (1, 2, 5 and 10) are in three conserved noncoding sequences (4, 2 and 1) and are thus candidates for the functional regulatory polymorphisms that underlie the differences in Mina expression that distinguish strains with high or low TH2 bias. The identification of Mina-regulatory polymorphisms will provide candidates for the causative Dice1.2 genetic lesion and a foothold for delineation of the critical 'upstream' pathways.

Although differences in Mina expression can explain the Il4- and TH2 bias–regulatory activity of Dice1.2, it remains possible that other genes in the minimal Dice1.2 interval contribute to the TH2 bias–regulatory activity of Dice-1.2. Furthermore, Dice1.2 is one of two Il4- and TH2 bias–regulatory loci originally identified on chromosome 16 (the other being Dice1a, called 'Dice1.1' here)28. Thus, identification of the molecular basis of the action of Dice1.1 will probably add further mechanistic insight into the complex regulation of Il4 and TH2 bias. Notably, Dice1.2 (but not Dice1.1) is tightly linked genetically to a host response–modifying locus (LmrA) for the protozoan parasite Leishmania major that is responsible for leishmaniasis28. As TH2 bias is critical in determining susceptibility to leishmaniasis, it is possible that Mina is LmrA. In this context, it is perhaps relevant that among hematopoietic cell types, Mina is expressed in CD4+ T cells and dendritic cells; the latter cell type has also been suggested to contribute to the different TH2-bias phenotypes of BALB/c and B10.D2 mice. A dual TH2 bias–regulatory function for Mina (with separate activities in naive helper T cells and dendritic cells) could explain the linkage of Dice1.2 but not Dice1.1 to LmrA. Investigation of the function of Mina in dendritic cells may thus provide further insight into the mechanism of TH2 bias.

Our data have identified a previously unknown IL-4-repressive pathway in which Mina serves a key function in regulating the amount of IL-4 produced by naive helper T cells, thereby controlling the extent of TH2 differentiation and TH2 bias. Natural genetic variation in this pathway contributes to the variation in TH2 bias characteristic of distinct inbred mouse strains. It will be important to determine the 'upstream' regulators, 'downstream' targets and repressive mechanism of Mina and the extent to which the Mina pathway may be conserved and manipulated in humans.

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Methods

The Methods and their associated references appear only online.

Accession codes.

UCSD-Nature Signaling Gateway (http://www.signaling-gateway.org): A001262, A001263, A002236, A001640 and A000024; Reference Database of Immune Cells of the Research Center for Allergy and Immunology50: microarray data, RMSPTB007001 and RMSPTB008001.

Note: Supplementary information is available on the Nature Immunology website.

* In the version of this article initially published online, the second corresponding author initials were incorrect. The correct initials are "M.Ku." The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgments

We thank R. Abe (Science University of Tokyo) for hybridoma PV-1; J. Allison (Memorial Sloan Kettering Cancer) for hybridoma 37N51.1; G. Trinchieri (US National Insitutes of Health) for hybridoma C17.8; A. Matsuno, M. Nakamura, M. Natsume, J. Epler, Y. Zhang, N. Li, S. Brown and R. Cross for technical help; J. Partridge for discussions; and D. Green, H. Beere and J. Kang (U. Mass. Medical School) for comments on the manuscript. Supported by the Cancer Research Institute (M.B.), the Burroughs Wellcome Fund (M.B.), American Lebanese Syrian Associated Charities (M.B.), the RIKEN Research Center for Allergy and Immunology International Collaboration Award Program (M.B. and M.Ku.), a Grant-in-Aid for Scientific Research (B) (M.Ku.), a Grant-in-Aid for Scientific Research on Priority Areas of the Ministry of Education, Culture, Sports, Science, and Technology (Japan) (M.Ku.), the Program for Promotion of Fundamental Studies in Health Sciences of the National Institute of Biomedical Innovation (M.Ku.) and the US National Institutes of Health (AI048636 to M.B.).

Author Contributions

M.O. and M.V.S. did the experiments; L.C. did the Mina transcriptional analysis and Figures 2b and 3b and Supplementary Figure 2; M.Ka. did the Mina immunoblots; X.S. analyzed the C16D2/8D mice; Y.S. did the transgenic experiments; Y.S. and L.C. maintained the mouse colonies; O.O., H.K. and A.H. did the expression profiling; M.O., M.V.S., M.Ku and M.B. designed and conceptualized the research and analyzed the data; and M.B. prepared the manuscript.

Received 2 September 2008; Accepted 6 May 2009; Published online 28 June 2009; Corrected 5 July 2009.

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  1. Laboratory for Signal Network, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Yokohama, Japan.
  2. Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
  3. Department of Immunology, University of Washington, Seattle, Washington, USA.
  4. Laboratory for Immunogenomics, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Yokohama, Japan.
  5. These authors contributed equally to this work.

Correspondence to: Mark Bix2 e-mail: mark.bix@stjude.org

Correspondence to: Masato Kubo1 e-mail: raysolfc@rcai.riken.jp

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Online methods

Mice.

Animals were bred and maintained in specific pathogen–free conditions in accordance with the guidelines of the Institutional Animal Care and Use Committees of St. Jude Children's Research Hospital and the RIKEN Institute. BALB/c, C57BL/6, C3H/HeN, B10.D2, DBA/2J, DBA/1J and DBA/2N mice were from Jackson Laboratory, Taconic Farms, CLEA and Charles River Laboratories.

Reagents and antibodies.

Anti-TCRbeta was purified from hybridoma H57.597. Anti-CD28 was purified from hybridomas PV-1 and 37N51.1 (gifts from R. Abe and J. Allison, respectively). Anti-IL-4 was used as purified protein or 10% culture supernatant from hybridoma 11B11. Anti-IL-12 was used as purified protein or 10% culture supernatant from hybridoma C17.8 (a gift from G. Trinchieri). Other antibodies were as follows: anti-Mina (M532; 40–9500; Zymed)46, 47; anti-NFATc2 (NFAT1-NFATp; 25A10.D6.D2; Tamar Laboratory Supplies), anti-NFATc1 (NFAT2; sc-13033; Santa Cruz), anti-Oct1 (sc-232; Santa Cruz,), anti-actin (sc-1616; Santa Cruz), anti-rabbit secondary antibody (SC-2305, Santa Cruz), horseradish peroxidase–conjugated anti-goat secondary antibody (SC-2020; Santa Cruz) and isotype control immunoglobulin G (AB46540-1; Abcam). Human recombinant IL-2 was used at a concentration of 20 U/ml. Mouse recombinant IL-4 was from PeproTech.

Expression profiling.

CD4+ T cells isolated from spleen and lymph nodes were stimulated with plate-bound monoclonal anti-TCRbeta (1 mug/ml; H57.597) and monoclonal anti-CD28 (10 mug/ml; 37N51.1). After 24 h, total RNA was extracted (Tri reagent, Sigma-Aldrich) and was purified on RNeasy minicolumns (Qiagen), then cRNA was synthesized according to Affymetrix protocols. Biotinylated cRNA was hybridized to an Affymetrix GeneChip (Mouse Genome 430 2.0 Array; Affymetrix). Microarray data were globally normalized with GeneSpring software (Agilent Technologies).

Quantitative RT-PCR.

First, cDNA was synthesized from total cellular RNA with SuperScript III reverse transcriptase (Invitrogen). Then, MX4000 (Stratagene) and 7500 (Applied Biosystems) real-time PCR systems were used for quantitative RT-PCR analysis (primer sequences, Supplementary Table 1), and mRNA expression was normalized to the expression of Actb or Hprt1.

Congenic mouse strains and phenotypic screening of TH2 bias.

The generation of congenic strain C16D2/8 has been described28. C16D2/8D mice were selected from the backcross progeny of C16D2/8 times BALB/c crosses. The congenic interval in C16D2/8D was bred to homozygosity by intercrossing and was characterized by genotyping (markers, Fig. 1a and Supplementary Table 1). Splenic CD4+ T cells isolated by magnetic cell sorting (CD4+ T cell Isolation kit; Miltenyi) were stimulated for 16 h with plate-bound anti-TCRbeta (1 mug/ml; H57.597) and anti-CD28 (10 mug/ml; 37N51.1), then RNA was collected (Tri reagent; Sigma-Aldrich) and expression of Il4 and Hprt1 was analyzed by real-time RT-PCR as described41, 51. In some experiments, splenic CD4+ T cells were isolated with the IMag magnetic cell separation system (BD) and were stimulated for 24 h with plate-bound anti-TCR (1 mug/ml; H57.597) and soluble anti-CD28 (PV-1; 10 mug/ml) before collection of RNA.

Immunoblot analysis.

Naive helper T cells were stimulated with PMA and ionomycin. Nuclear and cytoplasmic proteins were isolated from 15 times 106 cells with the NE-PER nuclear and cytoplasmic extraction reagent (78833; Pierce). Nuclear and cytoplasmic proteins (15 mug each) were separated by 12% SDS-PAGE, transferred to nitrocellulose membranes and hybridized to anti-Mina and anti-actin. After reaction with horseradish peroxidase–conjugated anti-rabbit secondary antibody (SC-2305; Santa Cruz), blots were visualized with chemiluminescence substrate (Roche). Mina expression is presented relative to actin expression.

Transient reporter assay.

Mina cDNA from strain B10.D2 was inserted into pCMV10 (Sigma-Aldrich) to generate the pCMV-FLAG-Mina expression construct. The 68-41 T cell hybridoma cells were cotransfected with plasmids encoding firefly luciferase driven by the Il4 or Il2 promoter (pIL-4-Luc and pGL-2), pCMV10 or pCMV-FLAG-Mina and a pancreatic alkaline phosphotase expression plasmid (pSVPAP; included to control for transfection efficiency). At 40 h after transfection, cells were stimulated for 12 h with plate-bound monoclonal anti-TCR (H57.597) and total cell lysates were prepared. Luciferase activity measured with a Microplate luminometer (Promega) is presented relative to the activity of pancreatic alkaline phosphotase.

EMSA.

EL4 cells or CD4+ T cells (enriched from B10.D2 or C57BL/6 spleen and lymph nodes) were stimulated with either PMA (Sigma) and ionomycin (Sigma) or plate-bound anti-TCRbeta (10 mug/ml; H57.597) and anti-CD28 (20 mug/ml; 37N51.1) in the presence or absence of cyclosporin A (1 mug/ml; Calbiochem52). Nuclear extracts were prepared with the NE-PER extraction kit according to the manufacturer's directions (Pierce). Protein concentrations were measured by the Bradford assay (Pierce) with BSA as a standard. Oligonucleotides were annealed in annealing buffer (100 mM Tris, pH 7.5, 10 mM EDTA, 2 M NaCl and 50 mM MgCl2) by heating to 95 °C followed by slow cooling to 22 °C. For gel shifts, annealed oligonucleotides were end-labeled with [gamma-32P]ATP and T4 polynucleotide kinase (Promega). Nuclear extracts (10 mug) or BSA, 32P-labeled oligonucleotide (1 times 104 c.p.m.) and poly(dI:dC) (125 ng; Sigma) were incubated together for 30 min at 22 °C in 20 mul binding buffer (10 mM Tris, pH 7.5, 60 mM KCl, 2 mM MgCl2 and 0.15 mM dithiothreitol). For 'supershifting', 2–3 mug antibody was included in the reaction. Binding reactions were resolved by electrophoresis through 1 times TAE–4% polyacrylamide gels.

DNA precipitation.

Precipitation assays were done as described53. Streptavidin-agarose beads (300 mul, Pierce) were preabsorbed with BSA (500 mul; 1 mg/ml), poly(dI:dC) (50 mug; Sigma) and sheared salmon sperm DNA (50 mug), then were washed three times and were resuspended in EMSA binding buffer (300 mul). Annealed 5' biotin–labeled oligonucleotides (1 mug) were incubated for 30 min at 22 °C with nuclear extracts (300 mug) from EL4 cells stimulated for 4 h PMA and ionomycin, in EMSA binding buffer along with poly(dI:dC) (10 mug). Then, preabsorbed beads (30 mul) were added to the oligonucleotide-protein mixture, followed by incubation for 4 h at 4 °C. DNA-protein-streptavidin-agarose complexes were washed three times with EMSA binding buffer, eluted in Laemmeli buffer, resolved by 12% SDS-PAGE, transferred to nitrocellulose membranes and blotted with anti-Mina (1 mug/ml) and anti-NFATc2 (1:5000 dilution; 25A10.D6.D1; Tamar Laboratory Supplies).

ChIP.

Equivalent-mass and equivalent-volume methods were used for ChIP. For the equivalent-mass method54, DNA recovered from an aliquot of sheared chromatin was used as the 'input' sample. The remaining chromatin was precleared with protein A and protein G agarose (16-156 and 16-266; Upstate) and then was incubated overnight at 4 °C with anti-Mina (2 mug/ml, 40–9500; Zymed). DNA recovered after immunoprecipitation was isolated with a PCR purification kit (QIAGEN) and was quantified by PicoGreen assay (Molecular Probes). An equivalent mass of immunoprecipitated and input DNA was analyzed by real-time PCR as described above for RT-PCR with the following modifications: Taq polymerase was from Qiagen (Hot Start), and cycling conditions were 94 °C for 15 min, followed by 45 cycles of 94 °C for 20 s, 61 °C for 1 min and 72 °C for 40 s. Data are presented as the ratio of the change-in-threshold (CT) value for immunoprecipitated DNA to that of input DNA.

For the equivalent-volume method55, chromatin prepared as described above was incubated overnight at 4 °C with anti-Mina or control immunoglobulin G (10 mug/ml; ab4640-1; Abcam). Input DNA and DNA recovered after immunoprecipitation were isolated with a PCR purification kit (QIAGEN). Then, 10 mul of immunoprecipitated DNA or 10 mul of a 1:20 dilution of input DNA was analyzed by real-time PCR as described above for RT-PCR with the following modifications: Taq polymerase was from Sigma, and the cycling conditions were 94 °C for 15 min, followed by 45 cycles of 94 °C for 20 s, 61 °C for 1 min and 72 °C for 40 s. Data are presented as the ratio of the change-in-threshold value for immunoprecipitated DNA to that of input DNA.

Mina-transgenic mice.

For the establishment of Mina-transgenic mice, B10.D2 Mina cDNA was cloned downstream of an element composed of the proximal promoter and Emu enhancer of the gene encoding Lck in the p1026X expression vector56. PCR of genomic DNA obtained from tail tissue identified ten independent BDF1 times C57BL/6 transgenic founders. Transgene copy number was determined by Southern blot analysis. Three founders containing over ten copies of the transgene were selected and were backcrossed for three generations to the BALB/c strain before further analysis. Protein expression in splenic CD4+ T cells was confirmed by immunoblot analysis with anti-Mina (40–9500; Zymed).

Antisense morpholino–mediated knockdown.

CD4+ T cells were enriched from C57BL/6 spleen and lymph nodes by complement-mediated lysis with antibody to heat-stable antigen (anti-CD24; J11d), anti–major histocompatibility complex class II (BP107) and anti-CD8 (53.67.2) and then were incubated overnight with Endo-Porter reagent57 (6 mul/ml) and fluorescein isothiocyanate–labeled standard control or Mina-morpholino (10 muM; Gene-Tools; Supplementary Table 1) in the presence of IL-7 (3 ng/ml). The transfection efficiency was over 80% as determined by flow cytometry. CD4+ T cells were then activated for 24 h with plate-bound anti-TCR (H57.597) and anti-CD28 (37N51.1) in the presence of IL-2 (25 U/ml) before immunoblot analysis of the knockdown of Mina and actin and quantitative RT-PCR analysis of the expression of Il4 and Ifng.

Gene annotation.

Gene annotation in the D16MIT138–MB04 interval was retrieved from the Mouse Genome Database (Mouse Genome Informatics, The Jackson Laboratory; May, 2009)30.

Statistical analysis.

Prism software was used for nonparametric t-tests.

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