Transcriptional unit of the murine Thy-1 gene: different distribution of transcription initiation sites in brain

Genetic labeling of neuronal subsets through enhancer trapping in mice

The ability to label, visualize, and manipulate subsets of neurons is critical for elucidating the structure and function of individual cell types in the brain. Enhancer trapping has proved extremely useful for the genetic manipulation of selective cell types in Drosophila. We have developed an enhancer trap strategy in mammals by generating transgenic mice with lentiviral vectors carrying single-copy enhancer-detector probes encoding either the marker gene lacZ or Cre recombinase. This transgenic strategy allowed us to genetically identify a wide variety of neuronal subpopulations in distinct brain regions. Enhancer detection by lentiviral transgenesis could thus provide a complementary method for generating transgenic mouse libraries for the genetic labeling and manipulation of neuronal subsets.

SOD1 and TDP-43 animal models of amyotrophic lateral sclerosis: recent advances in understanding disease toward the development of clinical treatments

Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disease with no cure. Breakthroughs in understanding ALS pathogenesis came with the discovery of dominant mutations in the superoxide dismutase 1 gene (SOD1) and other genes, including the gene encoding transactivating response element DNA binding protein-43 (TDP-43). This has led to the creation of animal models to further our understanding of the disease and identify a number of ALS-causing mechanisms, including mitochondrial dysfunction, protein misfolding and aggregation, oxidative damage, neuronal excitotoxicity, non-cell autonomous effects and neuroinflammation, axonal transport defects, neurotrophin depletion, effects from extracellular mutant SOD1, and aberrant RNA processing. Here we summarise the SOD1 and TDP-43 animal models created to date, report on recent findings supporting the potential mechanisms of ALS pathogenesis, and correlate this understanding with current developments in the clinic.

Roles and regulation of Thy-1, a context-dependent modulator of cell phenotype

Thy-1 or CD90 is a glycophosphatidylinositol-linked glycoprotein expressed on the surface of neurons, thymocytes, subsets of fibroblasts, endothelial cells, mesangial cells and some hematopoietic cells. Thy-1 is evolutionarily conserved, developmentally regulated, and often has dramatic effects on cell phenotype; however, the effects vary between and in some cases within cell types and tissues, and between similar tissues in different species, indicating that the biological role of Thy-1 is context-dependent. Thy-1 exists in soluble form in some body fluids; however, the mechanisms of its shedding are unknown. In addition, Thy-1 expression can be regulated by epigenetic silencing. Because Thy-1 modulates many basic cellular processes and is involved in the pathogenesis of a number of diseases, it is important to better understand its regulation.

Thy-1 promoter hypermethylation: a novel epigenetic pathogenic mechanism in pulmonary fibrosis

Mechanisms regulating myofibroblastic differentiation of fibroblasts within fibroblastic foci in idiopathic pulmonary fibrosis (IPF) remain unclear. Epigenetic processes, including DNA methylation, produce heritable but potentially reversible changes in DNA or its associated proteins and are prominent in development and oncogenesis. We have shown that Thy-1 suppresses myofibroblastic differentiation of lung fibroblasts and that fibroblasts in fibroblastic foci are Thy-1(-). Epigenetic down-regulation of Thy-1 has been demonstrated in cellular transformation and clinical cancer. We hypothesized that epigenetic regulation of Thy-1 affects the lung fibroblast fibrogenic phenotype. RT-PCR, methylation-specific PCR (MSP), and bisulfite genomic sequencing were used to determine the methylation status of the Thy-1 promoter in Thy-1(+) and Thy-1(-) lung fibroblasts, and MSP-in situ hybridization (MSPISH) was performed on fibrotic tissue. Thy-1 gene expression is absent in Thy-1(-) human and rat fibroblasts despite intact Thy-1 genomic DNA. Cytosine-guanine islands in the Thy-1 gene promoter are hypermethylated in Thy-1(-), but not Thy-1(+), fibroblasts. RT-PCR and MSP demonstrate that, in IPF samples in which Thy-1 expression is absent, the Thy-1 promoter region is methylated, whereas in lung samples retaining Thy-1 expression, the promoter region is unmethylated. MSPISH confirms methylation of the Thy-1 promoter in fibroblastic foci in IPF. Treatment with DNA methyltransferase inhibitors restores Thy-1 expression in Thy-1(-) fibroblasts. Epigenetic regulation of Thy-1 is a novel and potentially reversible mechanism in fibrosis that may offer the possibility of new therapeutic options.

The Ly-6A (Sca-1) GFP transgene is expressed in all adult mouse hematopoietic stem cells

The Sca-1 cell surface glycoprotein is used routinely as a marker of adult hematopoietic stem cells (HSCs), allowing a >100-fold enrichment of these rare cells from the bone marrow of the adult mouse. The Sca-1 protein is encoded by the Ly-6A/E gene, a small 4-exon gene that is tightly controlled in its expression in HSCs and several hematopoietic cell types. For the ability to sort and localize HSCs directly from the mouse, we initiated a transgenic approach in which we created Ly-6A (Sca-1) green fluorescent protein (GFP) transgenic mice. We show here that a 14-kb Ly-6A expression cassette directs the transcription of the GFP marker gene in all functional repopulating HSCs in the adult bone marrow. A >100-fold enrichment of HSCs occurred by sorting for the GFP-expressing cells. Furthermore, as shown by fluorescence-activated cell sorting and histologic analysis of several hematopoietic tissues, the GFP transgene expression pattern generally corresponded to that of Sca-1. Thus, the Ly-6A GFP transgene facilitates the enrichment of HSCs and presents the likelihood of identifying HSCs in situ.

Cloning and Characterization of the Rat Gene Encoding GAP-43

GAP-43 is a gene expressed only in the nervous system. The protein product is believed to be important to neuronal growth and plasticity. Most, and likely all, neurons express high levels of GAP-43 during periods of neurite elongation. To initiate studies of GAP-43 gene regulation we have cloned the rat gene encoding GAP-43. The GAP-43 gene includes three exons. The first exon encodes only the amino terminal 10 amino acids, which corresponds to the membrane targeting domain of GAP-43. The second exon encodes a putative calmodulin binding domain and a protein kinase C phosphorylation site. The 5'-flanking sequence is unusual in that it lacks CAAT or TATA elements, and directs RNA transcription initiation from several sites. Some of the transcription start sites are used to a different degree in the central and peripheral nervous systems.

Expression of the Ly-6A (Sca-1) lacZ transgene in mouse haematopoietic stem cells and embryos

The Sca-1 surface glycoprotein is used routinely as a marker for haematopoietic stem cell enrichment. Two allelic genes, Ly-6A and Ly-6E, encode this marker and appear to be differentially regulated in haematopoietic cells and haematopoietic stem cells. The Sca-1 protein has been shown to be expressed at a greater frequency in these cells from Ly-6A strains of mice. To study the specific expression pattern and haematopoietic regulation of the Ly-6A gene, we constructed a 14 kb cassette from a genomic Ly-6A fragment, inserted a lacZ reporter gene and created transgenic mice. We found that the Ly-6A lacZ transgene was expressed in the haematopoietic tissues and predominantly in the T-lymphoid lineage. Some expression was also found in the B-lymphoid and myeloid lineages. We demonstrated functional haematopoietic stem cell enrichment by sorting for beta-galactosidase-expressing cells from the bone marrow. In addition, we found an interesting embryonic expression pattern in the AGM region, the site of the first haematopoietic stem cell generation. Surprisingly, when compared with data from Ly-6E lacZ transgenic mice, our results suggest that the Ly-6A cassette does not improve lacZ marker gene expression in haematopoietic cells.

Expression of the Ly-6E.1 (Sca-1) transgene in adult hematopoietic stem cells and the developing mouse embryo

The mouse hematopoietic marker Sca-1, encoded by the Ly-6E.1 and Ly-6A.2 genes, has been instrumental in the enrichment and characterization of the stem cell for the adult blood system. In the studies reported here, we use Ly-6E.1 genomic fragments to direct expression of a lacZ marker transgene in vivo to study Ly-6E.1 specific regulatory elements in the hematopoietic stem cell and to localize these cells in the developing mouse embryo. We demonstrate that a region approximately 9 kb downstream from the transcriptional start site is required for the distinct, restricted expression pattern of the Ly-6E.1-lacZ transgene within adult hematopoietic stem cells and embryos. We also demonstrate that viable and functional lacZ-expressing hematopoietic stem cells can be enriched by FDG staining and flow cytometric sorting. The Ly-6E.1-lacZ-mediated enrichment of hematopoietic stem cells from adult transgenic bone marrow in combination with the temporal expression pattern of the transgene in the pro/mesonephros suggest an intraembryonic site of development for these cells in the mouse.

DNA methylation: biology and significance

The modification of DNA by cytosine methylation is crucial for normal development. DNA methylation patterns are distinctive between tissues and are maintained with high fidelity during cell division. DNA methylation probably exerts its effects through alterations in chromatin structure, with a resultant effect on genetic transcription. 5-methylcytosine is also prone to spontaneous hydrolytic deamination to thymine. Whilst most G:T mismatches so produced are repaired, failure of mismatch repair leads to established mutation. Indeed, mutations that are the result of 5-methylcytosine transitions account for a disproportionate number of genetic mutations described in malignant and non-malignant disease. There is also evidence for substantial deregulation of DNA methylation in malignancy. Whether this deregulation is crucial for the transformation process, or simply an epiphenomenon associated with it, is still not established.

A dominant chromatin-opening activity in 5' hypersensitive site 3 of the human beta-globin locus control region

Single-copy human beta-globin transgenes are very susceptible to suppression by position effects of surrounding closed chromatin. However, these position effects are overcome by a 20 kbp DNA fragment containing the locus control region (LCR). Here we show that the 6.5 kbp microlocus LCR cassette reproducibly directs full expression from independent single-copy beta-globin transgenes. By testing individual DNase I-hypersensitive sites (HS) present in the microlocus cassette, we demonstrate that the 1.5 kbp 5'HS2 enhancer fragment does not direct beta-globin expression from single-copy transgenes. In contrast, the 1.9 kbp 5'HS3 fragment directs beta-globin expression in five independent single-copy transgenic mouse lines. Moreover, the 5'HS3 core element and beta-globin proximal promoter sequences are DNase I hypersensitive in fetal liver nuclei of these expressing transgenic lines. Taken together, these results demonstrate that LCR activity is the culmination of at least two separable functions including: (i) a novel activity located in 5'HS3 that dominantly opens and remodels chromatin structure; and (ii) a recessive enhancer activity residing in 5'HS2. We postulate that the different elements of the LCR form a 'holocomplex' that interacts with the individual globin genes.

Developmental regulation of Thy 1.2 rate of synthesis in the mouse cerebellum

Thy 1.2 is a well-known major cell surface glycoprotein of the central nervous system (CNS). However, the regulation of the expression of this molecule as well as its function are yet to be determined. To approach these problems we studied the synthesis of the molecule in the developing cerebellum of wild-type and staggerer mutant mice. We found the appearance of a [35S]-methionine-labeled band detected with specific Sepharose 4B-bound monoclonal antibodies (Mabs). The Thy 1.2 activity increases progressively from postnatal day 9 (P9), reaching the highest rate at P12, subsequently decreasing sharply at P13, and remaining relatively low up to P16 in the wild type. Comparison of these data to the rates of total protein synthesis reveals a selective developmental regulation of Thy 1.2 expression, at least at the translational level. This correlates quite well with the timing of synaptic stabilization between parallel fibers and Purkinje cell dendritic spines. Furthermore, at P12 Thy 1.2 protein is preferentially located in the synaptosomal fraction. The parallel fiber:Purkinje cell synapsis is not stabilized in the staggerer mutant mouse. At P12 Thy 1.2 synthesis is 30% of the wild type, indicating that the translational regulation of Thy 1.2 is altered in the staggerer mutation.

Methylation status of CpG sites in the mouse and human CFTR promoters

To determine whether a relationship exists between DNA methylation and CFTR gene expression, we investigated the methylation status of CpG sites in the mouse and human CFTR promoters. Tissues and previously characterized cell lines that vary with respect to CFTR expression were selected for analysis using the methylation sensitive restriction endonuclease Hha I. We find that CpG sites are not methylated in high and low CFTR-expressing cell lines, whereas in the very low or non-CFTR-expressing cell lines, the CpG sites are partially or completely methylated. However, none of these sites were methylated in any of the tissues examined irrespective of the state of CFTR expression. Therefore, we conclude that the CFTR promoter belongs to the class of CpG-rich promoters in which the associated CpG sites are not methylated in tissues and that an inverse correlation between methylation and CFTR expression can only be found in cell lines.

De novo methylation of an MHC class I transgene following transformation with human adenoviruses is not correlated with its altered expression

The biological importance of class I histocompatibility antigens in a large variety of immune mechanisms is widely recognized, and their role in tumor rejection has been proven in several experimental tumor systems. Reduced expression of class I antigens, which is correlated with enhanced tumorigenicity, was shown in these systems to be mainly the result of transcriptional down-regulation. Mouse embryonal fibroblasts expressing H-2 antigens and the product of a miniature swine class I transgene, transformed by adenovirus 12, exhibit low levels of all class I antigens on the cell surface. Half of the cell lines demonstrate a suppressed level of class I mRNAs. Cell lines derived from transformation with the early region of adenovirus 5 express a high level of class I antigens. DNAs from adenovirus-transformed cells are extensively hypermethylated both in the 5' and the coding regions of the transgene compared to DNAs from immortalized cell lines and primary embryonal fibroblasts. Nevertheless, hypermethylation of these sequences is not correlated with mRNA level or cell-surface expression of the transgene product. Treatment of the transformed cells with high concentration of 5-azacytidine (5 Aza-C) induced merely a minor enhancement in the expression of class I mRNAs and class I antigens. Thus, this system is a perfect example of where viral transformation is associated with induced methylation of a class I gene, but hypermethylation does not affect its expression. The role of de novo methylation of genes in this system might be associated with transformation, or generation of mutations in CpG-rich sequences.

Regulation of Thy-1 gene expression by the methylation of the 5' region of Thy-1 gene and intracellular regulatory factors in immature B cells

In c mu- B220+ Thy-1- FL2-52-2, an immature B cell line transformed with a temperature-sensitive mutant of Abelson murine leukemia virus(ts OS-59), Thy-1 antigen expression was induced after the shift of the culture temperature from a permissive(35 degrees C) to a non-permissive temperature(39 degrees C), and a Thy-1+ subclone, FL2-52-2-1 was isolated by limiting dilution. Furthermore, since a population of Thy-1+FL2-52-2-1 lost Thy-1 antigen expression during culture at a non-permissive temperature, Thy-1- FL2-52-2-1-1 was isolated from the cultured cells. Methylation analysis by Southern blotting experiments showed that 5' region of the Thy-1 gene was methylated in Thy-1- FL2-52-2 but demethylated in Thy-1+ FL2-52-2-1 and Thy-1-FL2-52-2-1-1. To determine whether or not there exist intracellular regulatory factors responsible for Thy-1 gene expression, Thy-1a allele was transfected into Thy-1(Thy-1.2-) FL2-52-2 and Thy-1- FL2-52-2-1-1. The transfected Thy-1a allele was expressed in Thy-1- FL2-52-2, but not in Thy-1- FL2-52-2-1-1, indicating the presence of the intracellular regulatory factors requisite for Thy-1 gene expression in Thy-1- FL2-52-2. It appeared that in Thy-1- FL2-52-2-1-1, Thy-1 gene was not expressed because of the absence of the intracellular regulatory factors although the 5' region of the Thy-1 gene was demethylated. These results indicated the existence of at least two regulatory mechanisms of Thy-1 gene expression in immature B cells: methylation of the 5' region of the Thy-1 gene and intracellular regulatory factors.

Expression of the Neuronal Surface Glycoprotein Thy-1 Does Not Follow Appearance of Its mRNA in Developing Mouse Purkinje Cells

In developing rodent nervous system, although the appearance of Thy-1 mRNA, as seen by in situ hybridisation, is in general quickly followed by the appearance of immunohistochemically detectable protein, there are certain sites where a delay of several days occurs between expression of detectable message and protein. Mouse Purkinje cells exemplify this behaviour and are the dominant Thy-1-expressing cell in early postnatal cerebellum, so allowing quantitative, homogenate-based methods to be used to test whether such a lag in protein expression does occur. Measurement of Thy-1 mRNA (by slot blot) and protein (by radioimmunoassay) shows a substantial excess of Thy-1 message, compared to protein accumulating in the tissue, during the first postnatal week, which is not found in tissues (rat cerebellum, and rat or mouse cerebrum) where no lag is apparent in appearance of Thy-1 protein from the section-based methods. The species of Thy-1 mRNA produced by Purkinje cells does not appear to change during development, as assessed either in terms of its size (by northern blotting) or in the heterogeneous pattern of transcription initiation sites used (assessed by S1 nuclease protection analysis). Appearance of Thy-1 protein in these cells, therefore, seems to be regulated posttranscriptionally.

Differential methylation of a CpG-island concatemer in hemi- and homozygous transgenic mice

Methylation-free islands (MFIs), clusters of non-methylated CpG-dinucleotides in mammalian genomes, are associated with a majority of studied genes. By which precise mechanism they maintain their unmethylated status is unknown. The behaviour of transgenic MFIs may contribute to unveil this enigma. We have generated a high-copy number transgenic line with the MFI from the murine Thy-1.1 allele. A stable, minor fraction of this otherwise non-methylated DNA became completely methylated in all adult tissues tested. Furthermore, individuals homozygous for the transgene showed a significantly higher proportion of methylated copies compared to the hemizygous state. These findings support the hypothesis that a limited pool of trans-acting factors are involved in maintaining the hypomethylated state.

Identification of Thy-1 homologue in rabbit brain by immunoblot, immunohistochemistry and DNA/DNA hybridization

A membrane glycoprotein with an apparent molecular weight of approximately 26,000 reacted on immunoblot with a monoclonal antibody (HB-3S-17) directed toward human Thy-1. At cellular level, HB-3S-17 reacted with both rabbit and human cerebral cortexes in a similar manner as demonstrated by immunohistochemical staining. Screening of a rabbit brain expression cDNA library with HB-3S-17 resulted in the isolation of a clone designated RBT-2A-1. The rabbit cDNA insert of RBT-2A-1 hybridized in Southern blot with an oligonucleotide probe derived from the mouse Thy-1.2 gene. These data strongly indicate the existence of a glycoprotein in rabbit brain which is the counterpart of human and mouse Thy-1.

High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines

CpG islands are normally methylation free in cells of the animal, even when the associated gene is transcriptionally silent. In mouse NIH 3T3 and L cells, however, over half of the islands are heavily methylated. Near identity of the methylated subset in the two cell lines suggested that methylation is confined to genes that are nonessential in culture. In agreement with this, islands at several tissue-specific genes, but not at housekeeping genes, have become methylated in many human and mouse cell lines. At the chromatin level, methylated islands are Mspl resistant compared with their nonmethylated counterparts. We suggest that mutation-like gene inactivation due to CpG island methylation is widespread in many cell lines and could explain the loss of cell type-specific functions in culture.

Complex lymphoid and epithelial thymic tumours in Thy1-myc transgenic mice

T-lymphocyte development takes place mainly in the thymus, where stromal cells of epithelial and haemopoietic origin are involved in inductive and selective mechanisms, which enable specific lymphocyte populations to migrate to the periphery and establish a network of immune responses. Experiments with intact animals have clarified the precursor-product relationships between thymocyte subpopulations, but the molecular mechanisms of cell interactions in the thymus are difficult to study in vivo. In an attempt to expand thymic cell populations in vivo and maintain them in vitro for such studies, we directed high levels of expression of the murine c-myc proto-oncogene in transgenic mice by inserting it into the mouse Thy-1 transcriptional unit. Such mice develop thymic tumours which contain proliferating thymocytes and, interestingly, expanded populations of epithelial cells. Both cell types can be maintained in vitro.