NOR-2 (neuron-derived orphan receptor), a brain zinc finger protein, is highly induced during liver regeneration

Human glucocorticoid receptor isoform beta: recent understanding of its potential implications in physiology and pathophysiology

The human glucocorticoid receptor (GR) gene expresses two splicing isoforms alpha and beta through alternative use of specific exons 9alpha and 9beta. In contrast to the classic receptor GRalpha, which mediates most of the known actions of glucocorticoids, the functions of GRbeta have been largely unexplored. Owing to newly developed methods, for example microarrays and the jellyfish fluorescence proteins, we and others have recently revealed novel functions of GRbeta. Indeed, this enigmatic GR isoform influences positively and negatively the transcriptional activity of large subsets of genes, most of which are not responsive to glucocorticoids, in addition to its well-known dominant negative effect against GRalpha-mediated transcriptional activity. A recent report suggested that the "ligand-binding domain" of GRbeta is active, forming a functional ligand-binding pocket associated with the synthetic compound RU 486. In this review, we discuss the functions of GRbeta, its mechanisms of action, and its pathologic implications.

Naturally occurring C-terminal splice variants of nuclear receptors

Alternative mRNA splicing in the region encoding the C-terminus of nuclear receptors results in receptor variants lacking the entire ligand-binding domain (LBD), or a part of it, and instead contain a sequence of splice variant-specific C-terminal amino acids. A total of thirteen such splice variants have been shown to occur in vertebrates, and at least nine occur in humans. None of these receptor variants appear to be able to bind endogenous ligands and to induce transcription on promoters containing the response element for the respective canonical receptor variant. Interestingly, ten of these C-terminal splice variants have been shown to display dominant-negative activity on the transactivational properties of their canonical equivalent. Research on most of these splice variants has been limited, and the dominant-negative effect of these receptor variants has only been demonstrated in reporter assays in vitro, using transiently transfected receptors and reporter constructs. Therefore, the in vivo function and relevance of most C-terminal splice variants remains unclear. By reviewing the literature on the human glucocorticoid receptor beta-isoform (hGRbeta), we show that the dominant-negative effect of hGRbeta is well established using more physiologically relevant readouts. The hGR beta-isoform may alter gene transcription independent from the canonical receptor and increased hGRbeta levels correlate with glucocorticoid resistance and the occurrence of several immune-related diseases. Thus, available data suggests that C-terminal splice variants of nuclear receptors act as dominant-negative inhibitors of receptor-mediated signaling in vivo, and that aberrant expression of these isoforms may be involved in the pathogenesis of a variety of diseases.

Microarrays and expression profiling in microglia research and in inflammatory brain disorders

Expression profiling by using microarrays is a powerful tool for investigating transcriptional changes in a variety of diseases. In this survey, microarray data selected from the literature from in vivo and in vitro studies are scrutinized to find differentially expressed genes in common within specific inflammatory conditions in brain or microglial cell cultures, if there are at least two independent investigations available. Viral encephalitis, multiple sclerosis, epileptic seizures, ischemic lesions, and traumatic brain injury are the disorders covered. Moreover, by taking into account expression data obtained from cultured microglia, two examples are presented of how one can deal (or should not deal) with lists of candidate genes showing up in these kinds of studies without sophisticated software programs. Finally, some general remarks are made about pivotal issues when beginning to use microarray technology.

Altered mRNA expression of genes related to nerve cell activity in the fracture callus of older rats: A randomized, controlled, microarray study

Background

The time required for radiographic union following femoral fracture increases with age in both humans and rats for unknown reasons. Since abnormalities in fracture innervation will slow skeletal healing, we explored whether abnormal mRNA expression of genes related to nerve cell activity in the older rats was associated with the slowing of skeletal repair.

Methods

Simple, transverse, mid-shaft, femoral fractures with intramedullary rod fixation were induced in anaesthetized female Sprague-Dawley rats at 6, 26, and 52 weeks of age. At 0, 0.4, 1, 2, 4, and 6 weeks after fracture, a bony segment, one-third the length of the femur, centered on the fracture site, including the external callus, cortical bone, and marrow elements, was harvested. cRNA was prepared and hybridized to 54 Affymetrix U34A microarrays (3/age/time point).

Results

The mRNA levels of 62 genes related to neural function were affected by fracture. Of the total, 38 genes were altered by fracture to a similar extent at the three ages. In contrast, eight neural genes showed prolonged down-regulation in the older rats compared to the more rapid return to pre-fracture levels in younger rats. Seven genes were up-regulated by fracture more in the younger rats than in the older rats, while nine genes were up-regulated more in the older rats than in the younger.

Conclusions

mRNA of 24 nerve-related genes responded differently to fracture in older rats compared to young rats. This differential expression may reflect altered cell function at the fracture site that may be causally related to the slowing of fracture healing with age or may be an effect of the delayed healing.

Analysis of gene expression following norepinephrine stimulation in the rat pineal gland using DNA microarray technique

Several studies have demonstrated that norepinephrine (NE) is the critical neurotransmitter for the regulation of gene expression in the pineal gland. We studied the acute effect of NE stimulation in cultured rat pineal glands using Affymetrix rat genome microarray GeneChip probe arrays. Our data demonstrate that NE stimulation affects regulation of several genes; 44 and 29 genes were up- or down-regulated more than 2.5-fold, respectively. As shown in previous studies, arylalkylamine N-acetyltransferase, cyclic AMP responsive element modulator, jun-B and c-fos mRNA levels were increased by NE stimulation. Genes that were not previously reported and increased by NE stimulation in the pineal gland were protein tyrosine phosphatase, nuclear receptors, and activity and neurotransmitter-induced early genes. Unlike up-regulated genes, most of the down-regulated genes were not reported previously. Genes encoding enzymes involved in metabolism and structural proteins were decreased following NE stimulation. Identification of genes affected by NE stimulation would provide valuable information to understanding pineal biology fully.

Molecular genetic characterization of the EWS/CHN and RBP56/CHN fusion genes in extraskeletal myxoid chondrosarcoma

Extraskeletal myxoid chondrosarcoma (EMC) is a soft-tissue neoplasm cytogenetically characterized by the translocations t(9;22)(q22;q11-12) or t(9;17)(q22;q11), generating EWS/CHN or RBP56/CHN fusion genes, respectively. In the present study, 18 EMCs were studied both cytogenetically and at the molecular level. Chromosomal aberrations were detected in 16 samples: 13 with involvement of 9q22 and 22q11-12, and three with rearrangements of 9q22 and 17q11. Fifteen cases had an EWS/CHN fusion transcript and three had an RBP56/CHN transcript. The most frequent EWS/CHN transcript (type 1; 10 tumors), involved fusion of EWS exon 12 with CHN exon 3, and the second most common (type 5; two cases) was fusion of EWS exon 13 with CHN exon 3. In all tumors with RBP56/CHN fusion, exon 6 of RBP56 was fused to exon 3 of CHN. By genomic XL PCR and sequence analyses, the breakpoints from 14 cases were mapped in the EWS, RBP56, and CHN genes. In CHN, 12 breakpoints were found in intron 2 and only two in intron 1. In EWS, the breaks occurred in introns 7 (one break), 12 (eight breaks), and 13 (one break), and in RBP56 in intron 6. Repetitive elements such as Alu and LINE sequences seem to have limited, if any, importance in the genesis of EWS/CHN and RBP56/CHN chimeras. Furthermore, there were no chi, chi-like, topoisomerase II, or translin consensus sequences in the introns harboring the translocation breakpoints, nor could the number of topo I sites in EWS, RBP56, and CHN introns explain the uneven distribution of the breakpoints among EWS or CHN introns. Additional genetic events, such as nucleotide insertions, homologies at the junction, deletions, duplications, and inversions, were found to accompany the translocations, indicating that the chromosomal translocations do not require sequence-specific recombinases or extensive homology between the recombined sequences.

The AF2 domain of the orphan nuclear receptor TEC is essential for the transcriptional activity of the oncogenic fusion protein EWS/TEC

The EWS/TEC fusion protein encoded by the t(9:22) chromosomal translocation in human extraskeletal myxoid chondrosarcoma tumors is thought to participate in the tumoral process at least in part by deregulating the expression of specific target genes involved in the control of cell proliferation. In this work we show that the activation function-2 (AF2) domain of TEC is essential for the transcriptional activity of the EWS/TEC fusion protein. Significantly, deleting only the last 15 amino acids of the fusion protein, which contains 949 amino acids in its full form, results in a loss of over 70% of its transcriptional activity in transfected human chondrocyte cell lines. Point mutation analyses indicate that within the AF2 domain, amino acid residues I939, D940 and F943 all play a crucial role in the activity of EWS/TEC. Comparable results were obtained with the native TEC receptor. These results suggest that EWS/TEC interacts at least in part with the same transcriptional coactivators as the native TEC receptor, and that these coactivators may be involved in the tumoral process leading to human chondrosarcoma tumors.

Structure and expression of the mouse gene encoding the orphan nuclear receptor TEC

Translocated in extraskeletal chondrosarcoma (TEC) is an orphan nuclear receptor involved in the control of cell proliferation and apoptosis and is expressed mainly in the mammalian central nervous system. To help understand the regulation of its expression, we have characterized the mouse genomic locus encoding TEC and analyzed its expression pattern in various tissues. The gene spans approximately 40 kb and contains 8 exons, of which the first two are noncoding. The promoter region does not contain any identifiable TATA box or CCAAT box elements; however, several binding sites for the transcription factors cyclic AMP-responsive element binding (CREB) protein and Spl are present. Two types of transcripts generated by alternative splicing were characterized by RT-PCR: one encodes the full-length receptor of 627 amino acids; the other encodes a truncated receptor of 429 amino acids lacking the entire carboxyl-terminal domain. Northern blots and RT-PCR analyses showed that mRNAs encoding both isoforms are expressed in all mouse tissues examined, with the highest levels being found in the brain. This expression pattern suggests that TEC may perform some basic housekeeping cellular function in addition to its role in cell proliferation.

An isoform of Nurr1 functions as a negative inhibitor of the NGFI-B family signaling

NGFI-B, Nurr1 and NOR-1 constitute a distinct subfamily within the nuclear receptor superfamily. To clarify the transcriptional regulation by the NGFI-B family, we searched for other components that can bind to the NBRE response element, a known target sequence for these transcription factors. By low stringency hybridization using the DNA binding domain of NOR-1 as a probe, a C-terminal truncated Nurr1 isoform, named Nurr2, was isolated from a mouse MC3T3-E1 cell cDNA library. Nurr2 had a novel cryptic exon located upstream in the Nurr1 promoter region, and was generated by alternative splicing at exons 1, 2 and 6. The C-terminal region was encoded by frame-shifted exon 6, and so Nurr2 lacked the C-terminal sequences corresponding to the putative ligand binding domain or dimerization domain. Quantitative reverse transcriptase-PCR experiments confirmed the presence of the Nurr2 isoform in mouse, rat and human. It was, like Nurr1, highly expressed in the pituitary and the cerebral cortex. Nurr2 and Nurr1 were also concomitantly induced by forskolin in NIH3T3 cells. Functional analysis using a reporter gene, containing NBRE response elements, indicated that while the isoform was inactive by itself, it could inhibit transactivation by the members of the NGFI-B family. These results indicate that the C-terminal truncated isoform, Nurr2, may act as a negative regulator of the NGFI-B family signaling.

Alternative splicing generates isoforms of human neuron-derived orphan receptor-1 (NOR-1) mRNA

Neuron-derived orphan receptor-1 (NOR-1) is a novel member of the Nur77/NGFI-B subfamily within the nuclear receptor superfamily. Recently, several proteins closely related to NOR-1 have been described. To elucidate the relationships between NOR-1 and these closely related proteins, we analyzed the human NOR-1 gene and its transcripts by molecular cloning. We identified two variant NOR-1 transcripts in human skeletal muscles. One variant has a different 5'-untranslated region, and the other lacks C-terminal amino acid sequences corresponding to the putative ligand binding domain. These variant sequences share the common exon-intron boundary with NOR-1 mRNA, suggesting that they were generated from a single gene by alternative splicing, with the divergent points conserved between the rat and human. We also examined the promoter activities of the 5'-flanking regions of the two NOR-1 transcripts (NOR-1alpha and NOR-1beta mRNAs) by luciferase gene transfection. We demonstrated that the 5'-flanking region of the previously described NOR-1 gene, which has characteristics of a promoter found in housekeeping genes, showed potent promoter activity although the promoter for NOR-1beta mRNAs could not be determined.

Enhanced NOR-1 gene expression by exposure of Chinese hamster cells to high-density 50 Hz magnetic fields

Enhanced expression of neuron derived orphan receptor (NOR-1) gene was observed by exposure of Chinese hamster ovary K1 (CHO-K1) cells to an extremely low frequency magnetic field (ELFMF) of 50 Hz at 400 mT, but not at 5 mT. The enhanced expression, reaching the maximum at 6 h, was transient and reduced to the control level after exposure to 400 mT ELFMF for 24 h. The NOR-1 expression induced by treatment with forskolin and TPA was further enhanced by the simultaneous treatment with 400 mT ELFMF, in which the maximum response was at 3 h. The NOR-1 expression by these treatments was induced more earlier than that by 400 mT ELFMF alone. When cells were treated with an inhibitor of the protein kinase C (calphostin C or crocetin) and Ca2+ entry blockers (nifedipin and dantrolen) during the 400 mT ELFMF exposure, the enhanced NOR-1 expression was not observed. Exposure of CHO-K1 cells to the high-density 400 mT ELFMF may affect the signal transduction in the cells, resulting in the enhanced NOR-1 gene expression.

Hippocampal plasticity involves extensive gene induction and multiple cellular mechanisms

Long-term plasticity of the central nervous system (CNS) involves induction of a set of genes whose identity is incompletely characterized. To identify candidate plasticity-related genes (CPGs), we conducted an exhaustive screen for genes that undergo induction or downregulation in the hippocampus dentate gyrus (DG) following animal treatment with the potent glutamate analog, kainate. The screen yielded 362 upregulated CPGs and 41 downregulated transcripts (dCPGs). Of these, 66 CPGs and 5 dCPGs are known genes that encode for a variety of signal transduction proteins, transcription factors, and structural proteins. Seven novel CPGs predict the following putative functions: cpg2--a dystrophin-like cytoskeletal protein; cpg4--a heat-shock protein: cpg16--a protein kinase; cpg20--a transcription factor; cpg21--a dual-specificity MAP-kinase phosphatase; and cpg30 and cpg38--two new seven-transmembrane domain receptors. Experiments performed in vitro and with cultured hippocampal cells confirmed the ability of the cpg-21 product to inactivate the MAP-kinase. To test relevance to neural plasticity, 66 CPGs were tested for induction by stimuli producing long-term potentiation (LTP). Approximately one-fourth of the genes examined were upregulated by LTP. These results indicate that an extensive genetic response is induced in mammalian brain after glutamate receptor activation, and imply that a significant proportion of this activity is coinduced by LTP. Based on the identified CPGs, it is conceivable that multiple cellular mechanisms underlie long-term plasticity of the nervous system.

Retinoic acids differentially regulate NOR-1 and its closely related orphan nuclear receptor genes in breast cancer cell line MCF-7

NOR-1, NGFI-B, and Nurr1 are closely related orphan nuclear receptors implicated in diverse biological processes including cell growth and differentiation. We examined the effect of retinoic acids on the expression of these putative transcription factor genes in the breast cancer cell line MCF-7 by a quantitative reverse transcription and polymerase chain reaction. Both all-trans and 9-cis retinoic acids markedly induced NOR-1 mRNA and slightly increased Nurr1 mRNA. In contrast, NGFI-B mRNA was decreased. In the presence of cycloheximide, all-trans retinoic acid superinduced NOR-1 mRNA, whereas all-trans and 9-cis retinoic acids strongly suppressed the NGFI-B mRNA accumulation. The differential effects of retinoic acids on the expression of these genes are in contrast with the effects of forskolin and 12-O-tetradecanoylphorbol-13-acetate, both of which induced mRNAs of all three genes. These findings suggest that NOR-1, NGFI-B, and Nurr1 play distinct roles in the retinoic acid signaling in MCF-7 cells.

Structure, mapping and expression of a human NOR-1 gene, the third member of the Nur77/NGFI-B family

We identified a human homologue of NOR-1 (neuron-derived orphan receptor) from the fetal brain. There are two transcripts for human NOR-1, encoding 626 amino acid residues with a calculated molecular mass of 68 kDa. The high homology between hNOR-1, mNur77/rNGFI-B/hTR3, and mNurr1/rRNR-1/hNOT indicated that these three orphan receptors form a distinct subfamily within the steroid/thyroid receptor superfamily. Human NOR-1 mRNA was detected in the adult heart and skeletal muscle as well as in the fetal brain, indicating that its expression is not restricted to events that occur during neural development. The hNOR-1 gene is more than 35 kilobases long and interrupted by seven introns. The exon-intron structure of the gene is generally conserved when compared with the steroid/thyroid receptor superfamily and is remarkably similar to that of the Nur77/NGFI-B genes. This suggests that the Nur77/NGFI-B family has evolved from a common ancestral gene. Fluorescence in situ hybridization (FISH) revealed that the gene is located on chromosome 9q.