Genomic structure of the gene for mouse germ-cell nuclear factor (GCNF). II. Comparison with the genomic structure of the human GCNF gene.

BACKGROUND: Germ-cell nuclear factor (GCNF, NR6AI) is an orphan nuclear receptor. Its expression pattern suggests it functions during embryogenesis, in the placenta and in germ-cell development. Mouse GCNF cDNA codes for a protein of 495 amino acids, whereas the four reported human cDNA variants code for proteins of 454 to 480 amino acids. Apart from this size difference, there is sequence conservation of up to 98.7%. To elucidate the genomic structure that gives rise to the different human GCNF mRNAs, the sequence information of the human GCNF locus is compared to the previously reported structure of the mouse locus. RESULTS: The genomic structures of the mouse and human GCNF genes are highly conserved. The comparison reveals that the shorter human protein results from skipping the 45 base-pair third exon. Three different human isoforms - GCNF-1, GCNF-2a and GCNF-2b - are generated by differential usage of alternative splice acceptor sites of the fourth and the seventh exon. CONCLUSION: By homology with the mouse gene, 11 GCNF coding exons can be defined on human chromosome 9. All human GCNF cDNAs identified so far are, however, derived from mRNAs generated by splicing the fourth to the second exon. Although the genomic sequence is highly conserved, the analysis suggests that alternative splicing generates a higher complexity of human GCNF isoforms compared with the situation in the mouse.

Developmental expression of the estrogen receptor-related receptor gamma in the nervous system during mouse embryogenesis.

The ERR's (estrogen receptor-related receptors) are constitutive activators of the classical estrogen response element. In this report, we demonstrate that ERRgamma is highly expressed in the nervous system of the developing mouse embryo and that the adult pattern of expression of ERRgamma is, with few exceptions, established during embryogenesis. Transcripts are preferentially detected in already differentiating areas of the nervous system.

Differential expression of the estrogen receptor-related receptor gamma in the mouse brain.

To elucidate estrogen functions, the expression of the estrogen receptor-related receptor ERRgamma, a novel orphan nuclear receptor regulating transcription via estrogen responsive elements, has been localized by in situ hybridization in adult murine brain. ERRgamma transcripts were abundantly present in the isocortex, the olfactory system, cranial nerve nuclei and major parts of the coordination centers, e.g. reticular formation and major parts of the extrapyramidal motor systems. In addition, ERRgamma expression was detected in trigeminal ganglion neurons. ERRgamma distribution was clearly distinguished from that described for ERRalpha, for ERRbeta, and for estrogen receptors (ER) pointing at functional differences between ERRgamma and these receptors.

Alternative splicing and expression of the mouse estrogen receptor-related receptor gamma.

Estrogen receptor-related receptors (ERRs) are orphan members of the nuclear receptor superfamily, closely related to the estrogen receptor. With a PCR-based cloning strategy we have identified two cDNA isoforms from a neonatal mouse whole brain cDNA library encoding ERRgamma. We show that alternative splicing gives rise to different 5'-ends. The predicted peptide sequence of ERRgamma2 differs from ERRgamma1 by additional 23 N-terminal residues. The presence of identical isoforms in human suggests a pivotal function of ERRgamma in mammalia. Northern blot analysis reveals that ERRgamma is expressed as early as day 11 of embryonic development (E11). Whole mount in situ hybridization analysis shows major expression of ERRgamma in the central nervous system at E12.5. In the adult mouse a 5.7 kb transcript is detected in heart, brain, kidney, and skeletal muscle. Therefore, ERRgamma may be involved in the differentiation, as well as the maintenance of the differentiated properties in the brain.

Genomic structure of the gene for mouse germ cell nuclear factor (GCNF).

BACKGROUND: The germ cell nuclear factor (GCNF, also known as retinoid acid receptor-related testis-associated receptor, neuronal cell nuclear receptor or NR6A1) is an orphan receptor in the nuclear receptor superfamily found in mammals, amphibians and fish. The mouse Gcnf gene is expressed in the placenta and the developing nervous system and germ cells, and responds to retinoic acid. RESULTS: We have defined the intron-exon structure of the mouse Gcnf gene and found that it contains 11 exons. Exons 1-4 encode the 75 amino acid amino-terminal domain and exon 4 also encodes the core DNA-binding domain. The carboxy-terminal extension is encoded by exon 5, exons 6 and 7 encode the hinge region, and exons 7-11 encode the putative ligand-binding domain. Unusually, the two zinc-finger motifs in the DNA-binding domain are encoded by separate exons. CONCLUSIONS: The protein-coding region of GCNF is contained in 11 exons. The genomic structure of this nuclear receptor gene will be useful for further studies.

DNA binding, protein interaction and differential expression of the human germ cell nuclear factor.

The mouse germ cell nuclear factor (mGCNF) is an orphan nuclear receptor implicated in diverse biological processes, including gametogenesis, embryonic development and embryonal carcinoma cell differentiation. We have examined the binding and regulation of the human orthologue, hGCNF, expressed in the teratocarcinoma-derived cell line NTera-2/clone D1 (NT2/D1). Binding of GCNF to the direct repeat of the sequence -AGGTCA- (DR-0) is conserved in mammalia. The formation of interspecies dimers of the in vitro synthesized proteins suggests that cellular GCNF binding is mediated by homodimers. Both the mouse and the human protein bind in concert with cellular factors to DNA. Treatment of NT2/D1 cells with all-trans retinoic acid (atRA) is accompanied first by an up-regulation followed later by a down-regulation of hGCNF and its mRNA. Temporary up-regulation in NT2/D1 cells after treatment with atRA suggests that hGCNF is important for human neural determination and differentiation.

Retinoids induce differential expression and DNA binding of the mouse germ cell nuclear factor in P19 embryonal carcinoma cells.

The mouse germ cell nuclear factor (GCNF), a member of the nuclear receptor superfamily, is highly expressed during gametogenesis and in the developing nervous system. The in vitro translated protein binds as a homodimer to the direct repeat (DR) of the sequence -AGGTCA- (DR-0). In this report, we characterize a DR-0 binding activity in P19 cell extracts that is induced by retinoids. This induction is concentration dependent and specific for embryonal carcinoma cells. The cellular protein binds with the same specificity as in vitro expressed GCNF, but migrates as a slower complex, indicating interaction with partner proteins. Because antisera directed against GCNF recognize this complex, we propose that GCNF is part of the binding activity. Combining in vitro translated GCNF and extracts of non-expressing cells shows that such interactions can be formed posttranslationally. Northern analysis demonstrates a concentration dependent induction of GCNF mRNA by retinoic acid. A time course shows that the level of GCNF binding is transiently elevated, later downregulated, and not detectable in differentiated cells. We propose that GCNF regulation is an important step during determination of embryonal carcinoma cells.

Dimeric binding of the mouse germ cell nuclear factor.

The mouse germ cell nuclear factor (GCNF), a member of the nuclear receptor superfamily, is highly expressed during spermatogenesis, oogenesis, and during neuronal embryonic differentiation. The in vitro translated receptor binds autonomously to the direct repeat of the sequence 5'-AGGTCA-3'. To gain insights into the determinants necessary for DNA binding, I have generated truncated GCNF molecules by introducing carboxy-terminal deletions into expression constructs. An electrophoretic mobility-shift assay with these polypeptides shows that amino acids in addition to the core DNA-binding domain are important for specific binding. To address the question of whether the protein binds as monomer, homodimer, or heterodimer, I used different approaches. Analysis of the full-length protein was possible with GCNF polypeptides that contain epitopes of six consecutive histidines. Using a monoclonal antibody directed against these epitopes, I demonstrate that two GCNF molecules bind to a direct repeat. Dimerization between wild-type and truncated GCNF is shown by an electrophoretic mobility-shift analysis with a mixture of the proteins. In addition, I show that there is no in vitro interaction of GCNF with the retinoid X receptor, a promiscous partner of many nuclear receptors. The data suggest that GCNF may excert its in vivo function independently of other nuclear receptors.

The germ cell nuclear factor mGCNF is expressed in the developing nervous system.

Using a reinoic acid receptor hybridization probe, we have isolated a mouse embryonic cDNA that encodes the germ cell nuclear factor (mGCNF). The in vitro translated protein binds specifically to the direct repeat of the sequence-AGGTCA-which is characteristic of a subclass of nuclear receptors, albeit with a spacing of zero that is unique among the receptors. Northern analysis shows embryonic expression after mouse gastrulation and during early organogenesis, as well as expression in the adult testis. The message level decreases during embryonic development. Whereas there are two transcripts in the testis, only the larger one is found in embryos. In situ analysis of embryos at days 6.5-10.5 of gestation shows that, in the early postimplantation period, high transcript levels are found in ectodermal cells and in the primitive streak. During further development the expression becomes more restricted. Mainly cells of the developing nervous system are expressing the receptor. Our findings imply that GCNF is involved in two apparently disparate developmental events.

Characterization of the human germ cell nuclear factor gene.

A cDNA clone encoding the germ cell nuclear factor, GCNF, a member of the nuclear receptor superfamily has been isolated from the human embryonal carcinoma cell line NT2/D1. Sequencing of this clone reveals an open reading frame encoding a 476 amino acid protein. A comparison of the amino acid sequence of the human GCNF with its mouse homologue shows only six amino acid exchanges in the whole protein and a deletion in the amino-terminal region. Northern blot analysis demonstrates that the expression in the testis is conserved.

Identification of cis-acting elements as DNase I hypersensitive sites in lysozyme gene chromatin.

DNase I hypersensitive sites in chromatin of eukaryotic cells mark the positions of multifactorial cis-acting elements. Mapping DH sites by indirect end labeling is a convenient procedure used for identifying regulatory elements within extensive regions of chromatin and for gaining information about their functional specificity as well as their fine structure.

Differential expression and activation of a family of murine peroxisome proliferator-activated receptors.

To gain insight into the function of peroxisome proliferator-activated receptor (PPAR) isoforms in mammals, we have cloned and characterized two PPAR alpha-related cDNAs (designated PPAR gamma and -delta, respectively) from mouse. The three PPAR isoforms display widely divergent patterns of expression during embryogenesis and in the adult. Surprisingly, PPAR gamma and -delta are not activated by pirinixic acid (Wy 14,643), a potent peroxisome proliferator and activator of PPAR alpha. However, PPAR gamma and -delta are activated by the structurally distinct peroxisome proliferator LY-171883 and linoleic acid, respectively, indicating that each of the isoforms can act as a regulated activator of transcription. These data suggest that tissue-specific responsiveness to peroxisome proliferators, including certain fatty acids, is in part a consequence of differential expression of multiple, pharmacologically distinct PPAR isoforms.

The -6.1-kilobase chicken lysozyme enhancer is a multifactorial complex containing several cell-type-specific elements.

In the chromatin domain of the chicken lysozyme gene of myeloid and oviduct cells, which both have the potential to activate the gene, a developmentally stable DNase I-hypersensitive site is formed around 6.1 kb upstream of the gene. This implies that this DNA region, which has previously been demonstrated to function as a transcriptional enhancer element in myeloid cells, is intimately involved in the cell-type-specific activation of the lysozyme gene locus. Deletion analysis identifies a 157-bp minimal fragment that confers the same promacrophage-specific enhancer activity as the originally described 562-bp -6.1-kb enhancer fragment. By introducing specific point mutations, we demonstrate in transient gene transfer experiments that the minimal fragment consists of at least six adjacent elements, each substantially contributing to enhancer function. The compact multifactorial enhancer complex includes a nuclear factor I (NF-I)/TGGCA binding site, homologies to AP1, and octanucleotide or enhancer core consensus motifs. Point mutation of the NF-I binding site results in the loss of NF-I binding in vitro and enhancer activity in vivo after gene transfer. Surprisingly, four overlapping oligonucleotides, each consisting of at least two elements of the -6.1-kb enhancer, confer myeloid-cell-specific enhancer activity. We found several myeloid-cell-specific DNA-binding proteins interacting with the -6.1-kb enhancer, a result consistent with that described above. Therefore, we suggest that more than a single trans-acting factor mediates the cell type specificity of the -6.1-kb enhancer.

A mouse cdc25 homolog is differentially and developmentally expressed.

The timing and activation of the p34cdc2 kinase in mammals is associated with dephosphorylation of phosphotyrosine and phosphothreonine residues on the p34cdc2 kinase. For fission yeast, the timing of mitosis is regulated by cyclic accumulation of cdc25, which promotes dephosphorylation of p34cdc2 and concomitant protein kinase activation. We report the identification and characterization of a structural and functional mouse homolog, Cdc25M2, of the cdc25 phosphatase. Cdc25M2 shows high sequence identity to the previously reported human homolog cdc25Hu2. Cdc25M2 can functionally complement for a Schizosaccharomyces pombe cdc25ts mutation, and when expressed in Escherichia coli and purified, Cdc25M2 is an active phosphatase. cdc25M2 mRNA shows variation in expression in different tissues in the mouse embryo and is expressed in a developmental and cell-cycle-dependent fashion. We suggest that the expression and accumulation of the cdc25 mitotic inducer may play a critical role in the regulation of mouse development.

Characterization of three RXR genes that mediate the action of 9-cis retinoic acid.

An understanding of the differences and similarities of the retinoid X receptor (RXR) and retinoic acid receptor (RAR) systems requires knowledge of the diversity of their family members, their patterns of expression, and their pharmacological response to ligands. In this paper we report the isolation of a family of mouse RXR genes encoding three distinct receptors (RXR alpha, beta, and gamma). They are closely related to each other in their DNA- and ligand-binding domains but are quite divergent from the RAR subfamily in both structure and ligand specificity. Recently, we demonstrated that all-trans retinoic acid (RA) serves as a "pro-hormone" to the isomer 9-cis RA, which is a high-affinity ligand for the human RXR alpha. We extend those findings to show that 9-cis RA is also "retinoid X" for mouse RXR alpha, beta, and gamma. Trans-activation analyses show that although all three RXRs respond to a variety of endogenous retinoids, 9-cis RA is their most potent ligand and is up to 40-fold more active than all-trans RA. Northern blot and in situ hybridization analyses define a broad spectrum of expression for the RXRs, which display unique patterns and only partially overlap themselves and the RARs. This study suggests that the RXR family plays critical roles in diverse aspects of development, from embryo implantation to organogenesis and central nervous system differentiation, as well as in adult physiology.

A direct repeat in the cellular retinol-binding protein type II gene confers differential regulation by RXR and RAR.

The vitamin A derivative retinoic acid exerts its effects on transcription through two distinct classes of nuclear receptors, the retinoic acid receptor (RAR) and the retinoid X receptor (RXR). We provide evidence that expression of the gene for cellular retinol-binding protein type II (CRBPII), a key protein in the intestinal absorption of vitamin A, is dramatically up-regulated by retinoic acid in the presence of RXR but not RAR. This regulation is conferred through a specific cis element in the CRBPII promoter that contains five nearly perfect tandem repeats of the sequence AGGTCA spaced by a single nucleotide. The discovery of this new RX response element provides a means for distinguishing between the two retinoid receptor systems and suggests that an RXR-mediated pathway exists for modulating vitamin A metabolism.

Cloning of a novel glutamate receptor subunit, GluR5: expression in the nervous system during development.

We have isolated cDNAs encoding a glutamate receptor subunit, designated GluR5, displaying 40%-41% amino acid identity with the kainate/AMPA receptor subunits GluR1, GluR2, GluR3, and GluR4. This level of sequence similarity is significantly below the approximately 70% intersubunit identity characteristic of kainate/AMPA receptors. The GluR5 protein forms homomeric ion channels in Xenopus oocytes that are weakly responsive to L-glutamate. The GluR5 gene is expressed in subsets of neurons throughout the developing and adult central and peripheral nervous systems. During embryogenesis, GluR5 transcripts are detected in areas of neuronal differentiation and synapse formation.

TGGCA protein is present in erythroid nuclei and binds within the nuclease-hypersensitive sites 5' of the chicken beta H- and beta A-globin genes.

The developmentally regulated 5'-flanking DNase-I-hypersensitive site of the chicken beta H-globin gene in nuclei contains a subregion which is resistant to DNase I and which disappears when nuclei are extracted with 0.3 M NaCl, suggesting that there are salt-extractable proteins bound to sequences within this region. The 0.3 M NaCl extract contains two proteins which bind in vitro to these sequences. One of the binding sequences has an inverted repeat very similar to that bound by TGGCA protein. Partially purified TGGCA protein from chicken liver binds to this sequence in vitro giving exactly the same footprint as that obtained with erythroid nuclear proteins. Similarly TGGCA protein binds to an inverted repeat with the beta A-globin 5'-hypersensitive site giving a footprint identical to that obtained with erythroid nuclear protein extracts. From competition footprinting experiments and the electrophoretic mobility of the protein-DNA complex, it is concluded that the erythroid proteins previously described as binding to the beta H- and beta A-globin inverted repeats within the 5'-flanking hypersensitive sites both belong to the TGGCA protein family.

Viral myb oncogene encodes a sequence-specific DNA-binding activity.

The retroviral oncogene v-myb and its cellular progenitor c-myb encode nuclear DNA-binding proteins. Myb genes have been identified in a broad range of species, including vertebrates, the fruit fly Drosophila melanogaster and the plant Zea mays. The localization of the DNA-binding domain of the v-MYB protein to the highly conserved amino-terminal region suggests that the MYB/DNA interaction is important for MYB function. We show here that v-MYB specifically recognizes the nucleotide sequence pyAACG/TG. So like other nuclear transforming proteins, v-MYB seems to be a member of the class of sequence-specific DNA-binding factors presumably involved in gene regulation.

Interaction of the TGGCA-binding protein with upstream sequences is required for efficient transcription of mouse mammary tumor virus.

A high-affinity binding site for the TGGCA-binding protein, also known as nuclear factor I, has previously been shown to reside within the mouse mammary tumor virus (MMTV) long terminal repeat. We have introduced mutations into this binding site to test the importance of this ubiquitous nuclear protein in MMTV transcription. Mutations which abolish the binding of the TGGCA protein in vitro are shown to impair strongly glucocorticoid-induced transcription from this promoter in vivo. These data demonstrate that the TGGCA-binding protein is a multifunctional DNA-binding protein, capable of serving a transcriptional role in the case of MMTV, in addition to its known involvement in the replication of adenovirus.