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The Journal of Immunology, 1999, 162: 2820-2828.
Copyright © 1999 by The American Association of Immunologists

NF-ATc Isoforms Are Differentially Expressed and Regulated in Murine T and Mast Cells1 ,2

Melanie A. Sherman*, Doris R. Powell*, Deborah L. Weiss{ddagger} and Melissa A. Brown3,*,{dagger}

* Department of Experimental Pathology, and {dagger} Graduate Program in Immunology and Molecular Pathogenesis and Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, GA 30322; and {ddagger} Department of Chemistry, Williams College, Williamstown, MA 02167


    Abstract
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 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
NF of activated T cells (NF-AT) denotes a family of transcription factors that regulate the activation-dependent expression of many immunologically important proteins. At least four distinct genes encode the various family members, and several isoforms of these have been identified as well. The overlapping expression patterns and similar in vitro binding and trans-activation activities on various promoter elements of NF-AT-regulated genes suggest some redundancy in the function of these proteins. However, the phenotypic analysis of NF-AT-deficient mice supports the idea that there are tissue- and gene-specific functions as well. In this study we have characterized the expression of NF-AT cDNAs in murine mast cells. The majority of clones identified correspond to two NF-ATc isoforms that differ only in their amino-terminal sequence. Despite minimal discrepancies in the coding region, there are striking tissue- and cell type-specific differences in isoform expression patterns. Detection of NF-ATc.{alpha} mRNA is strictly dependent on cell activation signals in both T and mast cell lines. In contrast, the ß isoform is expressed at very low constitutive levels in both cell types but is only up-regulated in response to mast cell activation signals delivered through the Fc{epsilon}RI or via calcium ionophores. These results demonstrate another level of regulation within the NF-AT family that can contribute to cell type-specific gene expression.


    Introduction
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 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Nuclear factor of activated T cells (NF-AT)4 was originally described as a T cell-specific DNA binding protein that regulates the activation-dependent transcription of the IL-2 gene 1 . It is now known to denote a family of transcription factors that are expressed in a wide range of tissues and cell types, including mast cells 2 , B cells 3, 4, 5 , macrophages 6 , NK cells 7 , and neuronal cells 8 . Although most studies have focused on characterizing its role in the transcription of genes that regulate the immune system 9 , NF-AT also influences other processes such as cardiac development 10, 11 . Four family members, NF-ATp (NF-AT1) 12 , NF-ATc (NF-AT2) 13 , NF-AT3 14 , and NF-AT4/x/c3 14, 15, 16 , have been described. Three of the four NF-AT genes also give rise to multiple isoforms. Family members are defined by related DNA binding domains and conserved sequence motifs, including several serine/proline-rich regions that appear to regulate the nuclear localization of these factors 17, 18, 19 . All NF-AT proteins also appear to be a molecular target of the immunosuppressive drugs cyclosporin A and FK506 (for a review, see 9 . These agents interfere with the ability of calcineurin, a serine-threonine phosphatase, to dephosphorylate cytoplasmic NF-AT and thus prevent its shuttling to the nucleus in activated cells.

The existence of multiple NF-AT proteins that can recognize the same DNA element raises questions regarding their in vivo function. The overlapping expression patterns of some of these proteins and their similar in vitro binding and trans-activation activities on promoter elements of NF-AT-regulated genes argue that these factors are largely redundant. However, several lines of evidence support the idea that family members may also have cell-specific and/or gene-specific activities. 1) Outside the regions of high homology, the NF-AT family members have quite diverse sequences, providing the opportunity for interaction with unique cofactors required for the transcription of a subset of NF-AT-regulated genes. 2) Tissue-restricted expression of some individual family members and their isoforms has also been observed. For example, NF-AT3 is expressed at very low levels in the thymus, whereas NF-AT4 is strongly expressed at this site 14, 15, 16 . Likewise, isoforms of NF-AT3 show distinct expression patterns: the 3-kb form is expressed predominantly in the placenta, lung, kidney, testis, and ovary, and the 4.5-kb form is expressed in the heart and colon 14 . 3) Recent studies using antisera that can distinguish family members reveal the existence of NF-AT binding specificity. Timmerman et al. showed that while NF-AT1 and NF-AT2 can bind equally well to either the IL-2 or IL-4 promoter in in vitro DNA binding assays, NF-AT3 and NF-AT4 exhibit at least a 10-fold lower affinity 20 . Similarly, NF-ATx was shown to be the major component of IL-2 promoter DNA-protein complexes in double-positive thymocytes 21 .

The most compelling argument for gene-specific activities of NF-AT comes from the phenotypic analysis of NF-ATp- and NF-ATc-deficient mice. Stimulated T lymphocytes from NF-ATc-/- mice have an impaired ability to produce IL-4 22, 23 . The production of Ig isotypes associated with Th2 responses is also diminished 22 . Expression of other NF-AT-regulated genes in T cells, such as IL-2, was only slightly affected. These data demonstrate that IL-4 gene expression is a specific target of regulation by NF-ATc 22, 23 . In contrast, although the kinetics of IL-4 expression by activated T cells are delayed in NF-ATp-deficient mice, IL-4 production is significantly enhanced overall compared with that observed in wild-type animals. NF-AT4-/- animals produce relatively normal amounts of Th1 and Th2 cytokines such as IL-4, but positive selection of T cells is defective 22 . These results suggest the possibility that IL-4 transcription is positively regulated by NF-ATc and is repressed by NF-ATp 24, 25 .

In this study we provide evidence for cell-type specific expression of NF-ATc isoforms. These studies were prompted by our earlier observation that the NF-AT-mediated regulation of IL-4 gene transcription in mast cells exhibits striking differences compared with that of T cell IL-4 transcription 2 . Although the transcription of IL-4 in both cell types is dependent on an NF-AT site between -88 and -60 in the murine IL-4 gene, the protein-DNA complexes that form at this site are distinct. Unlike the T cell IL-4 complex that also contains activating protein-1 (AP-1), these Jun/Fos family members are not present in the mast cell NF-AT complex. DNA affinity purification and Western blot experiments also revealed differences in the size and regulation of the mast cell NF-AT protein associated with this site. These data suggested the possibility that this NF-AT was either a unique isoform or the product of a previously undescribed gene. Our efforts to address this issue led to the isolation of several NF-AT cDNA clones from a murine mast cell library. Here we report the full sequence of two murine NF-ATc isoforms, designated NF-ATc.{alpha} and -ß. Each form shows unique features in sequence and expression pattern compared with the previously described human NF-ATc genes 26 . In addition, murine T and mast cells exhibit striking differences in the relative expression of NF-ATc.{alpha} and NF-ATc.ß. This is due in part to the different inducibilities of these isoforms in response to TCR- and Fc{epsilon}RI-mediated signaling. The selective expression of NF-ATc isoforms may contribute to cell- and/or gene-specific transcription of molecules that function in inflammation and that have not been previously appreciated in knockout experiments.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Nucleotide sequence accession number

The sequences of the murine NF-ATc.{alpha} (accession no. AF087434) and NF-ATc.ß (accession no. AF049606) were deposited in the GenBank database.

cDNA cloning

A murine mast cell cDNA library was constructed in the {lambda}gt11 (Clontech, Palo Alto, CA.) vector. Poly(A)+ mRNA from stimulated (ionomycin for 90 min) CFTL15 mast cells 27 was used as the template for first-strand cDNA synthesis using both oligo(dT) and random hexamer primers. The library was screened at low stringency (2x SSC/0.5% SDS at 55°C) with a murine NF-ATp probe obtained by RT-PCR amplification of murine EL-4 T cell RNA. The probe contained sequences corresponding to nucleotides 1038–1517 within the rel similarity domain (RSD) of NF-ATp 28 . Positive clones were purified, and inserts were subcloned into pBluescript plasmids for further analysis. Sequencing of both strands of the cDNA inserts was performed using the dideoxynucleotide chain termination method with reagents from U.S. Biochemical Corp. (Cleveland, OH).

RNase protection analysis

Total RNA samples from cell lines and murine tissues (from unimmunized C3H/HeNCr mammary tumor virus (MTV)- mice) were isolated using the RNA-STAT reagent according to the manufacturer’s instructions (Tel-Test, Friendswood, TX). RNase protection assays were performed using NF-ATc.{alpha} (nucleotides 10–196 in the {alpha} sequence) and NF-ATc.ß (nucleotides 15–161 in ß sequence) cDNA fragments as templates for the synthesis of antisense RNA labeled to high sp. act. with [32P]UTP (Riboprobe kit, Promega, Madison, WI). Full-length RNA probes were gel-purified and hybridized (5 x 105 cpm) to 10 µg of total RNA overnight at 45°C in 40 mM PIPES (pH 6.4), 400 mM NaCl, 1 mM EDTA, and 80% formamide in a total volume of 30 µl. Samples were incubated for 1 h at 30°C after addition of 350 µl of digestion buffer (10 mM Tris (pH 7.5), 5 mM EDTA, 300 mM NaCl, 0.14 µg of RNase T1, and 1 µg of RNase A). Proteinase K (5 µl of 10 mg/ml stock) and SDS (10 µl of 20% solution) were added and incubated for an additional 30 min at 37°C. Samples were extracted with phenol/chloroform, precipitated, resuspended in gel loading buffer, and analyzed by 6% denaturing PAGE. Densitometric quantitation of relative mRNA expression levels was performed using the National Institutes of Health Image program.

Northern blot analysis

The murine tissue Northern blots were purchased from Clontech. For analysis of expression in cell lines, 10 µg of total RNA or 2 µg of poly(A)+ RNA was electrophoresed on a 1% formaldehyde gel and transferred to nitrocellulose. DNA probes were labeled by random hexamer priming and hybridized as described previously 29 . The NF-ATc-specific probe corresponds to nucleotides 1162–1727 based on the NF-ATc.ß sequence shown in Fig. 1Go and contains a significant portion of the RSD. The murine ß-actin probe includes nucleotides 147–332 of the published sequence 30 . The IL-4 cDNA probe corresponds to nucleotides 40–412 31 .



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FIGURE 1. Nucleotide and deduced amino acid sequence of murine NF-ATc.ß. Nucleotide sequences are numbered on the left, and amino acid sequences are numbered on the right. The nucleotides unique to the ß isoform are overlined.

 
Cells

CFTL15 is an IL-3-dependent murine mast cell line derived from fetal liver cells and was previously described 27 . Bone marrow-derived mast cells (BMMC) were isolated from BALB/c bone marrow cultured in IL-3 and stem cell factor. After 4 wk the cells were analyzed by flow cytometry for the surface expression of c-Kit and Fc{epsilon}RI. The c-Kit levels were determined using directly conjugated anti-CD117-phycoerythrin (PharMingen, San Diego, CA). Expression of the high affinity Fc{epsilon} was assessed using a two-step staining procedure. Cells were first incubated with purified mouse IgE (Sigma). After three washes, a second IgE bound to Fc{epsilon}R was detected using a rat anti-mouse IgE-FITC Ab (PharMingen). Data were acquired on a FACS caliber flow cytometer (Becton Dickinson, San Jose, CA) gating on propidium iodide-negative cells. Data were analyzed using CellQuest software (BDIS; Becton Dickinson). P815 and ABFTL3 are transformed mast cells that express IL-4 mRNA constitutively 29 . EL-4 is a murine thymoma line 32 that was obtained from American Type Culture Collection (Manassas, VA). D011.10 Th1 and Th2 cell lines were derived from the OVA-specific TCR transgenic mouse 33 . M12.4.1 B cells were a gift from Dr. Paul Rothman 34 ; L929 fibroblast cells were obtained from American Type Culture Collection and have been previously described 35 . Mast cells were activated by culturing with the calcium ionophore, ionomycin (1 µg/ml; Calbiochem, La Jolla, CA) or by cross-linking the high affinity Fc{epsilon}R by priming the cells with 1 µg/ml purified anti-DNP IgE (Sigma) for 2 h followed by activation with 5 µg/ml DNP-keyhole limpet hemocyanin (Calbiochem). In some experiments mast cells were cultured for 2 days with IgE before stimulation. T cells were stimulated with 1 µg/ml ionomycin and 20 ng/ml PMA (Sigma) or with Ag (2.5 x 105/ml BALB/c spleen cells, 104 U/ml IL-2, and 0.5 µM OVA323–339 peptide) for the indicated periods of time.


    Results
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 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Murine NF-ATc cDNAs encode {alpha} and ß isoforms that differ only at their N-termini

To identify NF-AT genes expressed in mast cells, a cDNA probe derived from the murine NF-ATp RSD was used to screen both oligo(dT)- and random hexamer-primed CFTL15 murine mast cell libraries at low stringency. Approximately 1.6 x 105 plaques were screened. Several clones were characterized, including one that corresponded to NF-ATp. The majority of the cDNAs analyzed were homologous to human NF-ATc.ß, an isoform identified in Raji B cells 26 . The longest clone is comprised of 3435 nucleotides, which includes an approximately 1.3-kb 3' untranslated region (3'UTR) that is unrelated to the 3'UTR of human NF-ATc (Fig. 1Go). Within the coding region, this cDNA exhibits >83% identity overall at the DNA level with the human gene (Fig. 2GoA). The cDNA encodes a protein of 704 amino acids (aa) with a predicted molecular mass of 70 kDa. A comparison of amino acid sequences reveals that NF-ATc is highly conserved in human and mouse. There is 96.7% identity and 98% similarity within the RSD (encoded by aa 408–684), which contains the DNA binding domain. The amino-terminal region (aa 1–407) contains three serine/proline (SP) motifs and is 83% identical and 91% similar to its human NF-ATc.ß homologue. A short C-terminal region (aa 685–704) does not show similarity to the reported sequence of human NF-ATc.



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FIGURE 2. A, Comparison of murine and human NF-ATc.ß cDNAs. The murine sequence is shown on the upper strand, and the human sequence is shown on the lower strand. The sequences were aligned using a blosum62 matrix (45 ). The RSD is boxed, and the SP boxes are shaded. B, NF-ATc isoforms differ only at the amino-terminal end. The unique amino acids that define the NF-ATc.{alpha} and -ß isoforms are shown. Within the N-terminal portion of NF-ATc.{alpha}, the methionines encoded by AUG codon within an optimal context for translation initiation (37) are underlined. NF-ATc.{alpha} cDNA isolated from murine T cells is reported to contain sequences encoding 3 additional aa (shown in brackets) including a potential ATG translation initiation codon (36). C, A comparison of the amino acid sequences that define the murine (top strand) and human (bottom strand) NF-ATc.{alpha} proteins. The sequences were aligned as described in A.

 
In addition to the ß isoform of NF-ATc, cDNAs encoding the murine NF-ATc.{alpha} homologue 13 were also isolated. It is notable that unlike the human cDNAs that encode isoform-specific amino acids at both the N- and C-terminal portions of the proteins 26 , the differences between murine NF-ATc.{alpha} and -ß were limited to the 5' end. In NF-ATc.{alpha} cDNAs, sequences specifying the first 27 aa of NF-ATc.ß are replaced by nucleotides that can potentially encode 39 {alpha} isoform-specific amino acids (Fig. 2GoB). The remainder of the cDNA sequence is identical with the ß isoform. While there is an in-frame AUG codon within this sequence, we were unable to obtain additional 5' sequence encoding an upstream methionine using several approaches. These include rapid amplification of 5' cDNA ends (RACE), direct screening of the cDNA library with a murine NF-ATc.{alpha} probe, and RT-PCR using murine T and mast cell cDNA and primers derived from the murine NF-ATc common region and the human NF-ATc.{alpha} 5'UTR. However, it is likely that these sequences exist. A recent report indicates that, like the human {alpha} isoform, a murine homologue isolated from T cells contains nucleotides that specify an additional 3 aa 36 . These sequences include an in-frame AUG codon in a context that is suboptimal for protein translation initiation (cggAUGc) 37 . This upstream AUG is used for the translation initiation of a minor NF-ATc protein species in human T cells. Our clones contain the downstream AUG, which lies in an optimal context (accAUGa) and initiates the major form of human NF-ATc.{alpha} translation 37, 38 . A comparison of the murine and human {alpha}-specific sequences shows that they share 80% identity and 80% similarity (Fig. 2GoC).

NF-ATc expression differs in human and murine tissues

Previous Northern blot analysis with human tissues, using probes that distinguish the {alpha} and ß isoforms, reveal that NF-ATc.ß mRNA is approximately 4.5 kb in size and is preferentially expressed in spleen, testis, and ovary; the {alpha} isoform is encoded by a 2.7-kb mRNA and is detected predominantly in the thymus and peripheral blood leukocytes 26 . In murine tissues, probes derived from both the 5' region (not shown) and the RSD (Fig. 3GoA) hybridize with two closely migrating mRNA species of about 4.5 kb, suggesting that both the {alpha} and ß isoforms mRNAs are of similar size. Levels of murine NF-ATc RNA are highest in spleen, lung, and skeletal muscle. Detectable, but much lower, expression was observed in heart, brain, liver, and kidney. There was no detectable expression in mouse testis, unlike results reported for human NF-ATc.



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FIGURE 3. A, Northern blot analysis of NF-ATc expression in murine tissues. The filter was hybridized with a probe corresponding to a portion of the RSD of murine NF-ATc. A murine actin probe was used as a loading control. The relative migration of the RNA size standards are indicated on the left. Arrows denote specific hybridizing bands. B, Northern blot analysis of NF-ATc expression in murine T and mast cell lines. Cells were left untreated (-) or were stimulated with ionomycin (mast cells), PMA and ionomycin (EL-4 T cells), or Ag (D011.10 T cells) for 3 h. Ten micrograms of total RNA were used for the analysis of most cell lines. Poly(A)+ RNA (2 µg) from CFTL15 mast cells was also included in this analysis. Hybridization of the blot was performed as described above.

 
A variety of T and mast cell lines were also analyzed for expression under resting and activated conditions. As shown in Fig. 3GoB, mRNAs of several sizes were observed. An approximately 4.5-kb band is the predominant species in both cell types and appears as an apparent doublet in mast cell lines. Consistent with studies in human cells demonstrating that NF-ATc expression is dependent on cell activation, no mRNA was detected in unstimulated T cells 13 . Several minor species appear to be expressed exclusively in mast cells. At least two mRNAs of about 3.0 kb were detected in activated mast cell lines. An additional 2.0 kb inducible mRNA was present in BMMC and P815 mast cells. Unstimulated L929 fibroblast cells and M12.4.1 B cells do not express detectable NF-ATc mRNA (data not shown).

NF-ATc.{alpha} and -ß mRNA are differentially expressed

Results from Northern analyses are consistent with the idea that there is cell- and tissue-specific expression of NF-ATc isoforms. RNase protection assays were performed using probes that can distinguish between the {alpha} and ß isoforms of NF-ATc to explore this possibility. The integrity of the RNA in the samples was verified in parallel reactions using a ß-actin probe (data not shown). As shown in Fig. 4Go, the ß isoform is strongly expressed in heart, spleen, and kidney, whereas {alpha}-specific mRNA is present only in spleen. Neither isoform is present at detectable levels in liver or brain. However, RNA samples from these tissues did protect a band of 70 bp corresponding to the region of the ß probe that is shared with {alpha}, indicating the presence of an additional isoform(s) of NF-ATc in the sample.



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FIGURE 4. Selective expression of NF-ATc.{alpha} and NF-ATc.ß in murine tissues. Ten-microgram aliquots of total RNA from the indicated tissues from unimmunized mice were used in RNase protection assays, using probes derived from the unique sequences of the NF-ATc.{alpha} and NF-ATc.ß cDNAs.

 
Differential expression of NF-ATc isoforms is also observed using RNA from cell lines. Significant expression of the {alpha} isoform is strictly dependent on cell activation in a variety of both T and mast cell lines (Fig. 5GoA). Stimulation through the Ag receptor or with PMA/ionomycin induces expression in DO11.10 Th1 and Th2 cells. EL-4 T cells also show significant expression in response to PMA/ionomycin activation. Cross-linkage of the high affinity Fc{epsilon} receptor or activation with calcium ionophore induces NF-ATc.{alpha} mRNA in BMMC and CFTL15 mast cells (Fig. 5Go, A and B). NF-ATc.{alpha} mRNA is only weakly expressed in P815 and ABFTL3 transformed mast cell lines.



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FIGURE 5. A and B, NF-ATc isoform expression is regulated by cell type-specific activation signals. Ten-microgram aliquots of RNA from the indicated cell lines were used in RNase protection assays as described in Fig. 4Go. CFTL15 and BMMC mast cell lines were stimulated with ionomycin or IgE/DNP for 3 h before RNA harvest. IgE x 2 indicates cultures that were preincubated for 2 days with IgE before subsequent IgE/DNP activation. EL-4 and D011.10 Th2 T cells were stimulated with PMA and ionomycin for 3 h. Ag-activated D011.10 Th1 and Th2 cells were cultured for 3 h with OVA peptide and splenic APCs before RNA harvest. Unstimulated cells were cultured under similar conditions but without Ag.

 
In contrast, the expression of significant NF-ATc.ß mRNA appears to be limited to normal mast cells; mast cells express low basal levels of steady state mRNA, which are significantly increased by stimulation with ionomycin or through IgE receptor cross-linking (Fig. 5Go, A and B). T cells also express detectable basal levels of the ß isoform mRNA. However, activation through either the Ag receptor or with PMA/ionomycin has little effect on the expression of NF-ATc.ß in these cells. The transformed mast cell lines P815 and ABFTL3 as well as L929 and M12 B cells express very low levels of NF-ATc.ß mRNA. Detection of signals in these cells requires long autoradiograph exposure times. These results indicate that induction of RNA encoding the two NF-ATc isoforms is differentially responsive to T and mast cell activation signals.

Steady state levels of NF-ATc isoforms are differentially regulated in activated T and mast cells

The apparent differences in NF-ATc inducibility between these distinct cell types could be explained simply by cell-specific differences in the kinetics of activation. To assess this possibility, T and mast cell lines were stimulated for various times, and total RNA was isolated for use in RNase protection assays. As shown in Fig. 6Go, maximal expression of NF-ATc.{alpha} was observed between 1 and 2.5 h, and then rapidly fell to undetectable levels in CFTL15 mast cells. In the T cell lines tested, the maximal expression of the {alpha} isoform message was observed between 2 and 3 h. There were also notable time-dependent differences in the expression of NF-ATc.{alpha} in the T cell lines; by 6 h poststimulation, little {alpha}-specific RNA was detected in Th1 cells, whereas detectable amounts persisted for at least 24 h after stimulation in Th2 cells and for 48 h in EL-4 cells.



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FIGURE 6. Kinetics of NF-ATc.{alpha} and -ß expression in response to activation signals. Cells were stimulated with ionomycin (CFTL15 cells), ionomycin and PMA (EL4 T cells), or OVA peptide and splenic APC (DO11.10 Th1 and Th2 cells). The last lanes in the DO11.10 panels (*) represent RNA after PMA/ionomycin stimulation for 3 h. RNA was isolated at the indicated times poststimulation and was used in RNase protection assays with {alpha} and ß isoform-specific probes as described in Fig. 4Go. Relative mRNA expression was quantitated by densitometry using the National Institutes of Health Image program. The mRNA levels in activated cells are expressed relative to unstimulated control values.

 
NF-ATc.ß mRNA was significantly increased within 30 min of cell activation and remained high through 6 h poststimulation in CFTL15 mast cells. The levels of NF-ATc.ß mRNA remained unaffected by activation in all T cells. These data confirm that the apparent differences in the inducible expression of NF-ATc.ß in T and mast cell lines are not due to differences in the kinetics of NF-ATc mRNA expression poststimulation, but rather to an inability of T cell activation signals to up-regulate NF-ATc.ß expression.

Cell type-specific differences in mRNA stability exist

To investigate the contribution of differences in mRNA stability to the cell-specific expression patterns we observed, CFTL15 mast cells and EL-4 T cells were stimulated for 2 h before treatment with actinomycin D to block ongoing transcription. Total mRNA was then isolated at 0.5-h intervals, and steady state levels were assessed by RNase protection. As shown in Fig. 7GoA, both NF-ATc.{alpha} and -ß mRNA persisted in CFTL15 mast cells at peak levels for at least 2 h after actinomycin D treatment. In fact, NF-ATc.{alpha} mRNA persisted much longer in actinomycin D-treated cells (Fig. 7GoB), suggesting that an mRNA-destabilizing product is transcribed concomitantly with NF-ATc in mast cells. NF-ATc.{alpha} mRNA expression in EL-4 cells is much more labile. Within 30 min of blocking transcription, levels of steady state mRNA are reduced by more than half. These data indicate that the persistence of NF-ATc.{alpha} expression in T cells is dependent in part on ongoing transcription.



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FIGURE 7. A, The mRNA stability of NF-ATc isoforms. CFTL15 mast cells and EL-4 T cells were stimulated as described above. At 2 h poststimulation, actinomycin D (Act D) was added to the cultures. Total RNA was harvested at 0.5-h intervals, and NF-ATc.{alpha} and ß expression was assessed by RNase protection assays. Relative expression levels were quantitated by densitometry as described in Fig. 6Go and are presented as a percentage of the mRNA observed at 2 h poststimulation. B, Comparison of NF-ATc.{alpha} mRNA persistence in untreated ({square}) and actinomycin D-treated mast cells (added at 2 h poststimulation; •). Relative mRNA levels from actinomycin D-treated CFTL15 mast cells (Fig. 7Go) and untreated cells (Fig. 6Go) were determined by densitometry as described above. Values at each time point are expressed as a percentage of the maximum inducible level observed at 2 h poststimulation, the time of addition of actinomycin D.

 

    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
In this report we describe the cloning and characterization of murine NF-ATc. Two variations of cDNA clones that are homologues of the previously described human NF-ATc.{alpha} and NF-ATc.ß isoforms were isolated from a murine mast cell library 13, 26 . Like the human isoforms, the murine cDNAs are distinguished by isoform-specific sequences at the 5' end of the coding region. These sequences are highly related to the human sequences. Murine NF-ATc.{alpha} and NF-ATc.ß cDNAs are otherwise identical and do not contain the isoform-specific differences in sequences 3' of the RSD that characterize the human sequences. In fact, the murine sequences located 3' of the RSD are unique and share no homology at the DNA or protein level with human NF-ATc.{alpha} and -ß. The murine NF-ATc.{alpha} DNA sequence reported here is similar, but not identical, with cDNAs derived from activated T cells reported by Pan et al. 36 .

In addition to the variants described in this report, it is likely that other NF-ATc isoforms exist. Although RNase protection assays demonstrate that brain and liver do not express appreciable amounts of either form, a protected band corresponding to the sequences encoding the common region was observed (Fig. 4Go). Similarly, several smaller mRNAs ranging in size from about 4.0 to <2.0 kb were easily detected in P815 cells by Northern blot analysis (Fig. 3GoB) despite the lack of an {alpha}- or ß-specific signal in these cells (Fig. 5Go, A and B). A subset of these small mRNA species was also observed in normal mast cells, suggesting that they are not unique to transformed mast cells. Western blot data likewise provide evidence for the existence of multiple protein isoforms of NF-ATc. We previously described a single anti-NF-ATc-reactive species of approximately 56 kDa in unstimulated mast cells and two additional proteins between 120 and 160 kDa whose expression is activation dependent 2 . In studies by Lyach et al., at least three proteins of distinct m.w. were observed in activated T cells using NF-ATc-specific antisera 38 . Whether these are generated by alternative splicing, the use of alternative promoters, or the selective utilization of translation start sites remains to be determined.

Why do multiple NF-ATc isoforms exist? We speculate that the unique regions of the NF-ATc isoforms confer distinct functions to these proteins. Structure-function studies have demonstrated that the N-terminal domain of NF-ATp (aa 1–415), human NF-ATc.{alpha} (aa 1–418), and the N- and C-terminal domains of NF-ATx function as trans-activation domains 39, 40, 41 . It is possible that unique domains act to attract unique coactivators. In support of this theory is the finding that p300/CREB binding protein can be recruited by NF-ATp 39 . In addition, we showed that AP-1 associates exclusively with the IL-4 promoter NF-AT complex in T cells but not in mast cells despite equivalent expression of these proteins in both cell types 2 . Proteins such as c-Maf, NF-AT-interacting protein-45, and GATA-3, which have been described as essential cofactors for IL-4 gene expression in T cells, are also candidates for a role in cell type-specific coactivation 42, 43, 44 . The existence of multiple isoforms that contain unique functional domains expands the potential repertoire of coactivators that can cooperate with NF-ATc to achieve selective gene expression in a given cell type.

Previous studies demonstrate that the regulation of NF-AT activity occurs at several levels (for a review, see 9 . All family members appear to undergo activation-dependent trans-location from the cytoplasm to the nucleus. These events require the calcium-dependent phosphatase, calcineurin, which acts on cytoplasmic NF-AT through direct protein-protein interactions and allows the shuttling of NF-AT to the nucleus. A nuclear kinase, glycogen synthase kinase-3, regulates the export of NF-AT back to the cytoplasm 19 . Tissue-specific expression patterns of NF-AT family members and their isoforms also regulate the range of NF-AT-responsive genes that can be influenced in any given cell type 9 . NF-ATp, NF-AT3, and NF-AT4/x are constitutively expressed in target tissues and are not subject to control by cell activation signals. In contrast, NF-ATc mRNA and protein expression are dependent on stimulation in human T cells 12, 13, 15, 16, 38 .

The results presented here demonstrate that additional levels of NF-AT regulation exist. In murine T cells and mast cells, activation through the TCR or high affinity Fc{epsilon}R is absolutely required for the expression of NF-ATc.{alpha}. In contrast, although the ß isoform is expressed at low constitutive levels in most of the cell lines we analyzed, only the mast cells demonstrate a significant increase in steady state mRNA levels upon stimulation. The clear-cut differences in expressions of the {alpha} and ß isoform mRNAs in response to activation signals support the hypothesis that distinct promoters responsive to T cell and/or mast cell activation signals contribute to the selective expression of these factors. We also provide evidence that mechanisms exist to differentially regulate mRNA half-life. Blocking transcription with actinomycin D prolongs the expression of NF-ATc.{alpha}, but not -ß, in mast cells, indicating that an active destabilizing agent functions to down-regulate steady state mRNA levels.

The analysis of cytokine responses in NF-ATc-deficient mice demonstrates that this factor is responsible for IL-4 production in activated T cells 10, 11 . Our data support the idea that NF-ATc.{alpha}, but not -ß, is involved in IL-4 transcription in Th2 cells. This conclusion is based on the observation that NF-ATc.ß is only minimally expressed in T cells and that the kinetics of NF-ATc.{alpha} closely parallel the expression of IL-4 in these cells (data not shown). Furthermore, cloning of NF-ATc from both human and murine T cells resulted in the isolation of cDNAs corresponding only to NF-ATc.{alpha}, indicating that this is the predominant NF-AT isoform expressed in this cell lineage 13, 36 .

Because the mast cell population was not affected by NF-ATc gene targeting in NF-ATc-/- mice, its in vivo role in mast cell IL-4 gene transcription has not been addressed. The current studies were initiated to identify the NF-AT factor(s) associated with the IL-4 promoter in mast cells. However, the identity of this factor is still elusive. DNA affinity purification experiments demonstrate that the major protein associated with the IL-4 NF-AT site between -88 and -60 is 41 kDa, a size not observed in analysis of anti-NF-ATc-reactive proteins by Western blot. Furthermore, this protein was reactive with NF-ATp antisera, although the specificity/cross-reactivity of both NF-ATp and NF-ATc antisera have not been rigorously tested. Given the prevalence of both isoforms in mast cells as well as activation kinetics that correlate with IL-4 expression, it is likely that NF-ATc plays a role. We are currently exploring the possibility that the shorter NF-ATc mRNAs encode this smaller protein associated with the IL-4 promoter in mast cells. A better understanding of the NF-ATc chromosomal gene will allow the targeting of isoform-specific sequences to assess their roles in vivo.


    Acknowledgments
 
We thank Tammy Nachman, who provided invaluable technical assistance with the experiments involving RNA isolation and Northern blot analysis and the maintenance of Ag-specific T cell lines. We also appreciate the assistance of Dr. Richard Lopez, who performed flow cytometric analyses to analyze the BMMC phenotype, Don Drake, who provided murine tissue samples for RNase protection analysis, Scott Sammons for help with the sequence analysis, and John Hural for computer graphics assistance.


    Footnotes
 
1 This work was supported by grants from the Multiple Sclerosis Society and the National Institutes of Health (CA47992), a scholarship from the Leukemia Society of America (to M.A.B.), and a fellowship from the Cancer Research Institute (to M.A.S.). Back

2 The sequences of the murine NF-ATc.{alpha} (accession no. AF087434) and NF-ATc.ß (accession no. AF049606) were deposited in the GenBank database. Back

3 Address correspondence and reprint requests to Dr. Melissa A. Brown, Department of Experimental Pathology, Emory University, 1639 Pierce Dr., Atlanta, GA 30322. E-mail address: Back

4 Abbreviations used in this paper: NF-AT, NF of activated T cells; Fc{epsilon}R1, high affinity Ig E receptor; RSD, rel similarity domain; BMMC, bone marrow-derived mast cells; UTR, untranslated region. Back

Received for publication September 1, 1998. Accepted for publication December 3, 1998.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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