An intron facilitates activation of the calspermin gene by the testis-specific transcription factor CREM tau

Identification and Characterization of the Very-Low-Density Lipoprotein Receptor Gene from Branchiostoma belcheri: Insights into the Origin and Evolution of the Low-Density Lipoprotein Receptor Gene Family

Low-density lipoprotein receptors (LDLRs) are a class of cell-surface endocytosis receptors that are mainly involved in cholesterol homeostasis and cellular signal transduction. Very-low-density lipoprotein receptors (VLDLRs), which are members of the LDLR family, have been regarded as multi-function receptors that fulfill diverse physiological functions. However, no VLDLR gene has been identified in protochordates to date. As a representative protochordate species, amphioxi are the best available example of vertebrate ancestors. Identifying and characterizing the VLDLR gene in amphioxi has high importance for exploring the evolutionary process of the LDLR family. With this study, a new amphioxus VLDLR gene (designated AmphiVLDLR) was cloned and characterized using RACE-PCR. The 3217 nt transcript of the AmphiVLDLR had a 2577 nt ORF, and the deduced 858 amino acids were highly conserved within vertebrate VLDLRs according to their primary structure and three-dimensional structure, both of which contained five characteristic domains. In contrast to other vertebrate VLDLRs, which had a conserved genomic structure organization with 19 exons and 18 introns, the AmphiVLDLR had 13 exons and 12 introns. The results of a selective pressure analysis showed that the AmphiVLDLR had numerous positive selection sites. Furthermore, the tissue expression of AmphiVLDLR using RT-qPCR showed that AmphiVLDLR RNA expression levels were highest in the gills and muscles, moderate in the hepatic cecum and gonads, and lowest in the intestines. The results of the evolutionary analysis demonstrated that the AmphiVLDLR gene is a new member of the VLDLR family whose family members have experienced duplications and deletions over the evolutionary process. These results imply that the functions of LDLR family members have also undergone differentiation. In summary, we found a new VLDLR gene homolog (AmphiVLDLR) in amphioxi. Our results provide insight into the function and evolution of the LDLR gene family.

An upstream region in the first intron of petunia actin-depolymerizing factor 1 affects tissue-specific expression in transgenic Arabidopsis (Arabidopsis thaliana)

The first intron of the petunia actin-depolymerizing factor 1 (PhADF1) gene was previously shown to induce strong and constitutive expression of that gene in vegetative tissues of transgenic Arabidopsis. To examine intron-mediated enhancement of PhADF1 gene expression in detail, the effects of splicing, deletion and promoter alteration on gene expression were analyzed in this study. Deletion of the 5' upstream region of the intron significantly reduced the level of enhancement, under the control of both the PhADF1 and the PhADF2 promoters. The ratio of pre-mRNA and mRNA does not correlate with the level of enhancement. To determine whether there is a promoter-intron interaction, the role of the intron was examined under the control of a heterogeneous promoter. The intron of PhADF1 induced GUS expression in vegetative tissues under the control of the reproductive tissue-specific Arabidopsis profilin 5 (PRF5) promoter. In transient assays, the presence of the intron increased GUS expression under control of the 35S minimal promoter. Our results suggest that the first intron of the PhADF1 gene alters tissue-specific expression by a post-transcriptional mechanism. In addition, we have also shown that intron-mediated enhancement is a conserved mechanism, which regulates the expression of the petunia and Arabidopsis ADF genes that are expressed in vegetative tissues.

Transcriptional regulation of CD4 gene expression by T cell factor-1/beta-catenin pathway

By interacting with MHC class II molecules, CD4 facilitates lineage development as well as activation of Th cells. Expression of physiological levels of CD4 requires a proximal CD4 enhancer to stimulate basic CD4 promoter activity. T cell factor (TCF)-1/beta-catenin pathway has previously been shown to regulate thymocyte survival via up-regulating antiapoptotic molecule Bcl-xL. By both loss and gain of function studies, in this study we show additional function of TCF-1/beta-catenin pathway in the regulation of CD4 expression in vivo. Mice deficient in TCF-1 displayed significantly reduced protein and mRNA levels of CD4 in CD4+ CD8+ double-positive (DP) thymocytes. A transgene encoding Bcl-2 restored survival but not CD4 levels of TCF-1(-/-) DP cells. Thus, TCF-1-regulated survival and CD4 expression are two separate events. In contrast, CD4 levels were restored on DP TCF-1(-/-) cells by transgenic expression of a wild-type TCF-1, but not a truncated TCF-1 that lacks a domain required for interacting with beta-catenin. Furthermore, forced expression of a stabilized beta-catenin, a coactivator of TCF-1, resulted in up-regulation of CD4. TCF-1 or stabilized beta-catenin greatly stimulated activity of a CD4 reporter gene driven by a basic CD4 promoter and the CD4 enhancer. However, mutation of a potential TCF binding site located within the enhancer abrogated TCF-1 and beta-catenin-mediated activation of CD4 reporter. Finally, recruitment of TCF-1 to CD4 enhancer was detected in wild-type but not TCF-1 null mice by chromatin-immunoprecipitation analysis. Thus, our results demonstrated that TCF/beta-catenin pathway enhances CD4 expression in vivo by recruiting TCF-1 to stimulate CD4 enhancer activity.

Basic helix-loop-helix transcription factor Tcfl5 interacts with the Calmegin gene promoter in mouse spermatogenesis

In mouse spermatogenesis, differentiating germ line cells initiate expression of specific genes at subsequent developmental steps. The Calmegin (Clgn) gene is first expressed in meiotic prophase, in primary spermatocytes, and encodes a protein that acts as a chaperone. To identify testis-specific transcription factors that control expression of the Clgn gene in spermatogenesis, we performed a yeast one-hybrid screening with a Clgn promoter sequence as bait DNA. This screening resulted in the identification of mouse Tcfl5 as a candidate Clgn promoter-binding protein. Tcfl5 is a member of the basic helix-loop-helix (bHLH) family of transcription factors, and mouse Tcfl5 shows 83% amino acid sequence identity with human TCFL5. Gel-shift and yeast one-hybrid experiments showed that Tcfl5 interacts with a non-canonical CACGCG site that is present in the Clgn promoter. By using northern blot, RT-PCR and in situ hybridization, mouse Tcfl5 mRNA was detected only in testis, with the highest expression level in primary spermatocytes and round spermatids. The highest level of Tcfl5 protein was found in primary spermatocytes at the diplotene stage of meiotic prophase, where the protein colocalizes with transcriptionally active chromatin.

Genomic structure and promoter activity of the testis haploid germ cell-specific intronless genes, Tact1 and Tact2

The Tact1 and Tact2 genes, each of which encodes an actin-like protein, are exclusively expressed and translated in haploid germ cells in testis. To characterize the haploid germ cell-specific gene structure, a mouse genomic library was screened with a Tact1 cDNA as a probe, and four independent phage clones containing the Tact1 gene were isolated. Southern hybridization and sequencing analyses revealed that Tact1 and Tact2 were single copy genes contained on a common fragment in a head-to-head orientation, and that the distance between these genes was less than 2 kb. Comparison of the nucleotide sequences of genomic DNA and cDNA demonstrated that Tact1 and Tact2 lack introns, although all known actin or actin-related genes in mammals contain introns. Human Tact orthologues also lack introns and are located within 6.4 kb in a head-to-head orientation. These findings indicate that Tact1 and Tact2 or one of these genes arose by retroposition of a spliced mRNA transcribed from an actin progenitor gene prior to the divergence of rodents and primates. The Tact1 and Tact2 genes are unusual retroposons in that they have retained an open reading frame and are expressed in testicular germ cells, because almost all retroposons become pseudogenes. It was revealed that a 2kb sequence between the two genes bidirectionally controls haploid germ-cell specific expression by analyzing transgenic mice. Comparison of the murine Tact genes with their human orthologues showed a high level of identity between the two species in the 5'-upstream and non-coding sequences as well as in the coding region, indicating that conserved elements in these regions may be involved in the regulation of haploid germ cell-specific expression. The promoter region contains no TATA-, CCAAT- or GC-boxes, although there are potential cAMP response element (CRE)-like motifs in the 5'-upstream region and the 5'-untranslated region in Tact1 and Tact2, respectively. Transient promoter analyses indicate that CREMtau may activate Tact1 and Tact2 expression in germ cells.

Genetic dissection of corticosterone receptor function in the rat hippocampus

The hippocampus, a brain structure with a crucial role in learning and memory and an involvement in stress-related neurological or psychiatric disorders, is extremely sensitive to aberrant levels of corticosteroid stress hormones (CORT). We hypothesized that CORT-affected brain disorders are the result of aberrant expression of specific CORT-responsive genes. In order to identify such genes, we have applied several gene expression profiling techniques such as differential display, DNA micro-arrays and in particular the highly sensitive serial analysis of gene expression (SAGE). Using SAGE, a total of 76,790 hippocampal tags were generated which together represent 28,748 unique mRNAs of which 4626 gave a hit with rat sequences in Genbank. By comparing SAGE profiles derived from rat hippocampi treated with different concentrations of corticosteroids, we have identified over 200 CORT-responsive genes with significant differential expression in hippocampus. The identified products include genes that are important for the plasticity of hippocampal neurones such as neural cell adhesion molecules, growth-promoting proteins, genes involved in axogenesis, synaptogenesis and signal-transduction. One novel corticosteroid-responsive gene, classified as Ca2+/calmodulin-dependent protein kinase (CaMK)-VI, exhibited structural resemblance with the family of CaMKs, in particular with that of CaMK-IV. We also identified an alternatively spliced mRNA of this gene encoding a peptide (CaMK-kinase related peptide or CARP) which may function in an autoregulatory feedback loop. These findings suggest a novel mode of operation of the CaMK pathway in control of Ca2+ homeostasis relevant for CORT-related brain disorders.

CaMKIV/Gr is dispensable for spermatogenesis and CREM-regulated transcription in male germ cells

The calcium/calmodulin-dependent protein kinase type IV/Gr (CaMKIV/Gr) is expressed in male germ cells and spermatids and has been implicated in controlling the differentiation of germ cells into mature spermatozoa. The function of CaMKIV/Gr in spermatogenesis was investigated using CaMKIV/Gr-deficient mice generated by targeted gene disruption. CaMKIV/Gr-deficient males exhibited normal spermatogenesis, and their fertility was similar to that of wild-type littermates. Notwithstanding the function of CaMKIV/Gr as an activator of cAMP response element (CRE)-dependent transcription, mRNA levels of several testis-specific CRE modulator (CREM)-regulated genes were unaltered. These results indicate that CaMKIV/Gr is not essential for spermatogenesis or for CRE-regulated gene transcription in the testis.

An E-box motif residing in the exon/intron 1 junction regulates both transcriptional activation and splicing of the human norepinephrine transporter gene

The norepinephrine transporter (NET) is responsible for the rapid NaCl-dependent uptake of norepinephrine into presynaptic noradrenergic nerve endings. Recently, we have characterized the structural organization of the 5' upstream promoter region of the human NET (hNET) gene. A new intron of 476 base pairs was found in the middle of the 5'-untranslated leader sequence and was shown to robustly enhance the promoter activity. Here, we show that the first hNET intron enhances both the homologous hNET and the heterologous thymidine kinase promoter activities in an orientation- and position-dependent manner. The first hNET intron exhibited a similar promoter-enhancing effect in both SK-N-BE(2)C (NET-positive) and HeLa (NET-negative) cell lines, showing that its function is not cell-specific. Transient transfection assays of a series of deletional constructs show that the first hNET intron contains subdomains with either positive or negative regulatory functions. Furthermore, DNase I footprinting analysis demonstrated that the 5' side of the intron, encompassing the splice donor site, is prominently protected by nuclear proteins isolated from both SK-N-BE(2)C and HeLa cells. The protected nucleotide sequence contains a consensus E-box motif, known to regulate diverse eukaryotic genes, which overlaps with the splice donor site of the first intron. We demonstrate that two basic helix-loop-helix proteins, upstream stimulatory factors 1 and 2, are major proteins interacting at this site and that the E-box is at least in part responsible for the promoter-enhancing activity of the first intron. Furthermore, site-directed mutagenesis of the splice donor site of the first intron affects both correct splicing and transcriptional activity. Taken together, our results indicate that a cis-element residing at the first exon/intron junction, encompassing an E-box motif, has a unique dual role in basal transcriptional activation and splicing of hNET mRNA.

Molecular and cellular mechanisms in spermatogenesis

Mammalian spermatogenesis shows a strict control of many specific molecular and cellular events. This control involves Sertoli cell-germ cell interaction, as well as a programmed performance of changes in chromatin structure and gene expression in the developing germ cells. In recent years, much knowledge about the functions of defined genes in spermatogenesis has been gained by making use of mouse transgenic and gene knockout models. Several of these models are discussed in this brief overview, with an emphasis on genes encoding proteins involved in the control of gene transcription, mRNA translation, DNA repair and protein ubiquitination. A better understanding of the molecular and cellular biology of spermatogenesis in the mouse may provide concepts that can improve our understanding of human male infertility and may also lead to the identification of novel targets for contraceptive intervention.

MEIG1 localizes to the nucleus and binds to meiotic chromosomes of spermatocytes as they initiate meiosis

Meiosis, the fundamental evolutionarily conserved differentiative process by which haploid gametes are produced, is a complex and tightly regulated nuclear process. The murine Meig1 gene was previously shown to have a germ cell-specific transcript which is abundantly expressed during meiosis, in both males and females, suggesting that it is involved in meiotic processes. Protein analysis revealed that MEIG1 appears in multiple phosphorylated forms, including two dimeric forms of M(r) 31,000 and 32,000, which exhibit a developmentally regulated switch in their relative abundance. The tyrosine-phosphorylated M(r) 31,000 form becomes the dominant form once the cells enter meiosis. In this study we show that the M(r) 31,000 dimeric form appears in the nuclear fraction of testicular protein extract, whereas the M(r) 32,000 dimeric form and the monomeric forms of MEIG1 remain cytoplasmic. The appearance in the nuclear fraction is developmentally regulated, coinciding with progression of the first spermatogenic wave through meiotic prophase I. Utilizing immunocytochemistry we show that nuclear localization is apparent in primary spermatocytes through their maturation into elongated spermatozoa, but not in either somatic cells or germ cells from early postnatal pups. We also show that MEIG1 associates specifically with meiotic chromosomes in vivo. These results indicate that in germ cells, the M(r) 31,000 dimeric form enters the nucleus during the first meiotic prophase and binds to the meiotic chromatin. Possible nuclear functions, as well as possible modes of nuclear localization, are discussed.

Identification of nuclear orphan receptors as regulators of expression of a neurotransmitter receptor gene

Nuclear orphan receptors are known to be important mediators of neurogenesis, but the target genes of these transcription factors in the vertebrate nervous system remain largely undefined. We have previously shown that a 500-base pair fragment in the first intron of the GRIK5 gene, which encodes the kainate-preferring glutamate receptor subunit KA2, down-regulates gene expression. In our present studies, mutation of an 11-base pair element within this fragment resulted in a loss of nuclear protein binding and reverses negative regulation by the intron. Using yeast one-hybrid screening, we have identified intron-binding proteins from rat brain as COUP-TFI, EAR2, and NURR1. Gel shift studies with postnatal day 2 rat brain extract indicate the presence of COUP-TFs, EAR2, and NURR1 in the DNA-protein complex. Competition assays with GRIK5-binding site mutations show that the recombinant clones exhibit differential binding characteristics and suggest that the DNA-protein complex from postnatal day 2 rat brain may consist primarily of EAR2. The DNA binding activity was also observed to be enriched in rat neural tissue and developmentally regulated. Co-transfection assays showed that recombinant nuclear orphan receptors function as transcriptional repressors in both CV1 cells and rat CG4 oligodendrocyte cells. Direct interaction of the orphan receptors with and relief of repression by TFIIB indicate likely role(s) in active and/or transrepression. Our findings are thus consistent with the notion that multiple nuclear orphan receptors can regulate the transcription of a widely expressed neurotransmitter receptor gene by binding a common element in an intron and directly modulating the activity of the transcription machinery.

Regional distribution of a novel calcium/calmodulin-dependent protein kinase mRNA in the rat brain

The regional distribution of a novel Ca(2+)/calmodulin-dependent protein kinase (CaMK-VI) was examined in the adult rat brain by in situ hybridization. High levels of CaMK-VI mRNA were detected in the hippocampus, piriform cortex and habenula, moderate levels in different thalamic nuclei and cerebral cortex, and low levels in the frontal and parietal cortex. This discrete distribution pattern suggests an important role for CaMK-VI in limbic brain regions.

A gene-targeting approach identifies a function for the first intron in expression of the alpha1(I) collagen gene

The role of the first intron of the Col1A1 gene in the regulation of type I collagen synthesis remains uncertain and controversial despite numerous studies that have made use of transgenic and transfection experiments. To examine the importance of the first intron in regulation of the gene, we have used the double-replacement method of gene targeting to introduce, by homologous recombination in embryonic stem (ES) cells, a mutated Col1A1 allele (Col-IntDelta). The Col-IntDelta allele contains a 1. 3-kb deletion within intron I and is also marked by the introduction of a silent mutation that created an XhoI restriction site in exon 7. Targeted mice were generated from two independently derived ES cell clones. Mice carrying two copies of the mutated gene were born in the expected Mendelian ratio, developed normally, and showed no apparent abnormalities. We used heterozygous mice to determine whether expression of the mutated allele differs from that of the normal allele. For this purpose, we developed a reverse transcription-PCR assay which takes advantage of the XhoI polymorphism in exon 7. Our results indicate that in the skin, and in cultured cells derived from the skin, the intron plays little or no role in constitutive expression of collagen I. However, in the lungs of young mice, the mutated allele was expressed at about 75% of the level of the normal allele, and in the adult lung expression was decreased to less than 50%. These results were confirmed by RNase protection assays which demonstrated a two- to threefold decrease in Col1A1 mRNA in lungs of homozygous mutant mice. Surprisingly, in cultured cells derived from the lung, the mutated allele was expressed at a level similar to that of the wild-type allele. Our results also indicated an age-dependent requirement for the intact intron in expression of the Col1A1 gene in muscle. Since the intron is spliced normally, and since the mutant allele is expressed as well as the wild-type allele in the skin, reduced mRNA stability is unlikely to contribute to the reduction in transcript levels. We conclude that the first intron of the Col1A1 gene plays a tissue-specific and developmentally regulated role in transcriptional regulation of the gene. Our experiments demonstrate the utility of gene-targeting techniques that produce subtle mutations for studies of cis-acting elements in gene regulation.

The olfactory adenylyl cyclase III is expressed in rat germ cells during spermiogenesis

To identify the adenylyl cyclase (AC) genes expressed in mammalian germ cells, RT-PCR of testis and germ cell RNA was performed using degenerated primers based on the homologous region of the AC catalytic domain. This strategy yielded high-frequency amplification of a complementary DNA (cDNA) identical to type III AC (ACIII), a form previously identified as the major adenylyl cyclase expressed in the olfactory system. Ribonuclease protection studies confirmed that ACIII transcripts are present in germ cells, appear during the meiotic prophase, and accumulate during spermiogenesis. A Northern blot analysis performed on total testis RNA demonstrated the presence of a predominant transcript of 7.5 kb, suggesting that the ACIII expressed in germ cells may derive from a splicing variant different from the 4.5 kb transcripts expressed in somatic cells. To determine whether these RNAs are translated into a protein, Western blot analysis was performed using an antibody specific for the carboxyl terminus of ACIII. An immunoreactive protein of 170 kDa was detected in extracts from total testis and from germ cells. Immunofluorescence localization of this protein in the seminiferous tubules showed that ACIII was predominantly expressed in postmeiotic germ cells from round spermatids in the cap phase to maturing elongating spermatids. The ACIII antigen was located mostly on the acrosomal membrane rather than on the plasma membrane of developing spermatids. The spatial and temporal expression of ACIII in germ cells indicates a role of this AC in the acrosome formation. Together with the observation that members of the olfactory receptor family and an olfactory phosphodiesterase are expressed in spermatids, these findings suggest that a signal transduction system used in olfaction is also used during gamete development.

Role of Ca++/calmodulin binding proteins in Aspergillus nidulans cell cycle regulation

The goal of this review is to summarise the current knowledge concerning the targets of Ca++/calmodulin that are essential for cell cycle progression in lower eukaryotes. Emphasis is placed on Aspergillus nidulans since this is the only organism to date shown to posses essential Ca++ dependent calmodulin activated enzymes. Two such enzymes are the calmodulin activated protein phosphatase, calcineurin and the calmodulin dependent protein kinase. These proteins, each the product of a unique gene, are required for progression of quiescent spores into the proliferative cycle and also for execution of the nuclear division cycle in exponentially growing germlings.

Novel repeat elements direct rat proenkephalin transcription during spermatogenesis

The developmental program controlling sperm formation occurs in multiple stages that sequentially involve mitosis, meiosis, and spermiogenesis. The transcriptional mechanisms regulating these distinct phases are poorly understood. In particular, while a required role for the germ cell transcription factor cyclic AMP response element modulator-tau during spermiogenesis has recently been demonstrated, the transcriptional mechanisms leading to early haploid cell formation are unknown. The rat and mouse proenkephalin genes are selectively expressed from an alternate, germ cell-specific promoter in meiotic and early haploid cells. In this study, the minimal rat proenkephalin germ line promoter was localized to a 116-bp region encompassing the transcriptional start site region. Further, a proximal 51-bp sequence located in the 5'-flanking region is absolutely required for germ line promoter activity. This 51 bp sequence corresponds to a previously characterized binding element (GCP1) that forms cell-specific complexes with rat spermatogenic cell nuclear factors distinct from cyclic AMP response element binding proteins. Further, GCP1 contains novel direct repeat sequences required for factor binding and transgene expression in spermatogenic cells. These repeat elements are highly similar to sequences within the active regions of other male germ line promoters expressed during meiosis. GCP1 may therefore contain transcriptional elements that participate more generally during meiosis in the differentiation of spermatocytes and early haploid spermatids.

Regulation of expression of the alpha 1 (I) collagen gene: a critical appraisal of the role of the first intron

The transcriptional regulation of the genes encoding the alpha 1 (I) collagen chains is necessarily complex since these genes are expressed at widely different levels, and in a cell- and tissue-specific fashion. In the case of the alpha 1 (I) gene, there is substantial, but controversial, evidence for an involvement of the first intron in the tissue-specific expression of the gene. This evidence is based largely on transfection of cells with collagen-reporter gene constructs and on studies of transgenic mice. In this review, I propose a number of reason for the conflicting data in the literature: 1) the cell-specific nature of the intronic effect; thus, not all cultured, collagen-synthesizing cells will demonstrate an intronic effect by transfection; 2) the possibility that functionally equivalent regulatory elements are placed in different regions of the alpha 1 (I) gene in different species; and 3) the possibility that functionally redundant sequences exist within the alpha 1 (I) gene, which would permit other regions to substitute for the first intron.

Organization and analysis of the complete rat calmodulin-dependent protein kinase IV gene

A 42-kilobase pair region of rat DNA containing the Ca2+/calmodulin-dependent protein kinase IV (CaM kinase IV) gene has been cloned and characterized. The gene consists of 12 exons and 11 introns and is predicted to encode both beta and alpha forms of CaM kinase IV as well as the testis-specific calmodulin-binding protein calspermin. The promoter utilized to generate the alpha-kinase isoform is located in intron 1, whereas the promoter utilized to produce the calspermin transcript is contained in intron 10. The calspermin promoter region which extends from -200 to +321 relative to the calspermin transcription initiation site that contains two cyclic AMP response elements (CRE) at -70 and -50 and has been shown previously to be inactive in NIH3T3 cells (Sun, Z., Sassone-Corsi, P., and Means, A. R. (1995) Mol. Cell. Biol. 15, 561-571) was ligated to the lacZ reporter gene and used to generate transgenic mice. The promoter was expressed exclusively in postmeiotic testis where beta-galactosidase was found predominantly in elongating spermatids. The cell and developmental specificity of transgene expression was very similar to the pattern shown by the endogenous gene. Although the transgene promoter was silent in somatic tissues, beta-galactosidase expression could be restored in primary cultures of skin fibroblasts by introduction of vectors encoding CREM tau and CaM kinase IV.