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Novel RNA family structure of hepatitis B virus expressed in human cells, using a helper-free adenovirus vector.

Ad5-HBL is a type 5 adenovirus bearing the large BglII fragment (2.8 kilobases; 87% of the total genome) of hepatitis B virus (HBV), subtype adr. Eight HBV RNAs expressed in HeLa cells infected with Ad5-HBL were mapped by the nuclease S1 technique. Three major RNAs spanning 2.4, 2.0, and 0.7 kilobases of the HBV sequences cover the coding regions of "presurface" plus surface antigen, surface antigen alone, and "X" protein, respectively. The 5' segment of an RNA which could code for core antigen (HBcAg) was also detected. All major HBV RNAs initiate from mutually exclusive 5' ends, terminate at the unique 3' end within the HBcAg coding region (except readthrough species), and have no spliced deletion, forming a novel RNA family structure. No TATA box-like sequences were found near the 5' end of these RNAs, except in the case of the 2.4-kilobase RNA. About two thirds of total HBV RNA does not terminate at the mapped 3'-end position, suggesting the termination signal is functionally inefficient. Since the potential 5' end of HBcAg mRNA was mapped at the same position as the minus-strand nick of HBV DNA previously reported, we propose a model that requires inefficient poly(A) addition to produce an RNA which serves both as HBcAg mRNA and as the putative RNA template of minus-strand DNA synthesis in the HBV life cycle.

Adenoviruses, Human↗

Characterization of an amyloid precursor protein-binding protein Fe65L2 and its novel isoforms lacking phosphotyrosine-interaction domains.

Human Fe65L2 is a member of the Fe65 protein family, which interacts with amyloid precursor protein (APP). Fe65L2 contains an N-terminal WW (Trp-Trp) domain followed by two phosphotyrosine-interaction domains, and consists of 486 amino acids. In the present study, we cloned and characterized two novel isoforms of Fe65L2, designated I-214 and I-245, which are produced by alternative splicing of the RNA. The splicing events disrupt the ability to bind with APP and low-density-lipoprotein-receptor-related protein. Fe65L2 was highly expressed in the brain, whereas I-214 and I-245 were expressed in various tissues. In HEK-293 cells, Fe65L2 was expressed in the nucleus and cytosol, whereas I-245 and I-214 were localized exclusively to the nucleus. The ratio of I-214 to Fe65L2 mRNA was increased by apoptotic stimuli. Although the overexpression of either Fe65L2 or I-214 did not significantly affect the half-life and maturation of APP, or the secretion of secreted APP, the secretion of beta-amyloid peptide (Abeta)40 and Abeta42 was increased by overexpression of Fe65L2, but not by that of I-214. These results suggest that Fe65L2 affects Abeta production and a possible regulation of Fe65L2 function by alternative splicing.

Alternative Splicing↗

Mantle cell lymphomas with low levels of cyclin D1 long mRNA transcripts are highly proliferative and can be discriminated by elevated cyclin A2 and cyclin B1.

The role of transcript variants of cyclin D1 in cancer biology is unclear. Most tumors with high levels of cyclin D1 express 2 transcripts due to alternative splicing: one full-length transcript of 4.4 kb and one short transcript of approximately 1.7 kb. The short transcript lacks part of the 3'UTR region regulating mRNA stability and has a longer half-life. In our study, the contribution of each of these mRNAs to gene expression and cell proliferation has been investigated in mantle cell lymphoma (MCL), a B cell lymphoma characterized by a specific gene translocation resulting in enhanced expression of cyclin D1. A subset of MCL tumors with low levels of the long cyclin D1 transcript (cyclin D1 3'UTR) was identified by quantitative PCR and by oligonucleotide array hybridization. This tumor-subset had 3.4-fold higher levels of the short form of cyclin D1 mRNA (p < 0.0001) and had higher expression of cyclin D1 protein. Gene expression analysis identified a number of cell-cycle regulatory genes as upregulated. There was a significant difference in frequencies of cyclin B1 (p = 0.0006) and cyclin A2 (p = 0.0006) positive cells that discriminated MCL with low cyclin D1 3'UTR from other highly proliferative MCL. Among differentially expressed genes, there was a highly upregulated gene with homology to the group of cell-cycle promoting E2F transcription partners, E2F_TDP5. Several of the upregulated genes, such as TOP2A, AURORA A and RRM2 may influence a response to therapy. Identification of MCL with low cyclin D1 3'UTR is important because it seems to be associated with shorter overall survival.

3' Untranslated Regions↗

Unregulated and basal transcriptional activities of the regulatory sequence of the type 18 human papillomavirus genome in transgenic mice.

Type 18 human papillomavirus (HPV18) is a genital virus closely associated with cervical carcinoma. To analyze the transcriptional activities of the long control region (LCR) of the HPV18 genome, we have produced 12 transgenic mice harboring the HPV18/LCR sequence fused to a promoterless SV40 T-antigen (TAg) gene. The mice were small in body size, generally very weak, and none lived longer than 110 days. Three mice with the longest life span (58-110 days) developed hyperplastic thymus and/or lymph node and were further analyzed. In these mice, Northern hybridization failed to detect TAg transcripts in any of the 25 organs studied. However, spliced TAg RNA was detected by polymerase chain reaction in the hyperplastic thymus and lymph node and in the normal submaxillary gland, stomach, large intestine, urinary bladder, and the cerebrum, indicating the presence of very low cellular levels of TAg RNA in these organs. When immunostaining was performed on the hyperplastic thymus, TAg protein was detected only in the ductal epithelial cells. Our results appear to indicate that the HPV18/LCR sequence was able to express only unregulated and basal levels of transcriptional activity in transgenic mice. Such a mode of transcription has become a major hindrance in the use of transgenic mouse system for the studies of the biology of the human papillomavirus.

Amino Acid Sequence↗

Structure of mRNA encoded by tubulin genes in Leishmania enriettii.

Both the alpha- and beta-tubulin genes of Leishmania enriettii are encoded by mRNA of 2.0-2.2 kb in length. We have shown previously that the alpha- and beta-tubulin genes are arranged in separate, tandem repeats of 2 and 4 kb, respectively, and now report the mapping of mature mRNA onto these cloned genes. Here we show that the alpha-tubulin gene contains a very short intergenic region (100-200 bases) whereas the larger, tandemly repeated beta-tubulin gene contains a 1.8-2.0 kb region not found in mature mRNA. Comparison of S-1 mapping and primer extension results indicates that the messenger RNAs for both alpha- and beta-tubulin contain a sequence of about 35 base pairs located at the 5' end that is not encoded contiguously with the rest of the mRNA. This short 5' sequence may be added to the body of the tubulin mRNAs either through splicing of a precursor RNA molecule or by a novel post-transcriptional processing reaction. The alpha- and beta-tubulin genes are arranged identically in the two developmental stages of the parasite life cycle and are present in equal copy number.

Animals↗

Characterization of the 415G>A (E139K) PMM2 mutation in carbohydrate-deficient glycoprotein syndrome type Ia disrupting a splicing enhancer resulting in exon 5 skipping.

Carbohydrate-deficient glycoprotein syndrome type Ia (CDGS) is an autosomal recessive disorder, characterized by a central nervous system dysfunction and multiorgan failure associated with defective N-glycosylation and phosphomannomutase (PMM) deficiency related to mutations in the PMM2 gene. A total of 26 different missense mutations and one single base pair deletion have already been described. We found by sequencing and restriction analysis, in two unrelated French patients with CDG type Ia a compound heterozygosity for two mutations in exon 5: a new mutation 415G>A (E139K) and the most frequent mutation 425G>A (R141H ). The 415G>A mutation disrupted a splicing enhancer sequence: (GAR)n-(GAR)n resulting in exon 5 skipping. We studied the activity of these mutant proteins expressed in E Coli. Compared to the normal PMM protein activity, the R141H and transcript without exon 5 expressed a protein with undetectable specific activity when the E139K mutant protein expressed a residual activity of 25%. The E139K mutant protein could be expressed at a sufficient level in vivo to confer residual activity compatible with life in these patients when absence of residual PMM activity is likely lethal.

Congenital Disorders of Glycosylation↗

Late-onset apparent mineralocorticoid excess caused by novel compound heterozygous mutations in the HSD11B2 gene.

Mutations in the gene encoding 11beta-hydroxysteroid dehydrogenase type 2, 11beta-HSD2 (HSD11B2), explain the molecular basis for the syndrome of apparent mineralocorticoid excess (AME), characterized by severe hypertension and hypokalemic alkalosis. Cortisol is the offending mineralocorticoid in AME, as the result of a lack of 11beta-HSD2-mediated cortisol to cortisone inactivation. In this study, we describe mutations in the HSD11B2 gene in 3 additional AME kindreds in which probands presented in adult life, with milder phenotypes including the original seminal case reported by Stewart and Edwards. Genetic analysis of the HSD11B2 gene revealed that all probands were compound heterozygotes, for a total of 7 novel coding and noncoding mutations. Of the 7 mutations detected, 6 were investigated for their effects on gene expression and enzyme activity by the use of mutant cDNA and minigene constructs transfected into HEK 293 cells. Four missense mutations resulted in enzymes with varying degrees of activity, all <10% of wild type. A further 2 mutations generated incorrectly spliced mRNA and predicted severely truncated, inactive enzyme. The mothers of 2 probands heterozygous for missense mutations have presented with a phenotype indistinguishable from "essential" hypertension. These genetic and biochemical data emphasize the heterogeneous nature of AME and the effects that heterozygosity at the HSD11B2 locus can have on blood pressure in later life.

11-beta-Hydroxysteroid Dehydrogenase Type 2↗

Alternative processing of RNA transcribed from NMYC.

NMYC is a gene whose amplification and overexpression have been implicated in the generation of certain human malignancies. Little is known of how the expression of NMYC is normally controlled. We have therefore characterized transcription from the gene and the structure and stability of the resulting mRNAs. Transcription from NMYC is exceptionally complex: it initiates at numerous sites that may be grouped under the control of two promoters, and the multiplicity of initiation sites combines with alternative splicing to engender two forms of mRNA. The mRNAs have different 5' leader sequences (alternative first exons of the gene) but identical bodies (the second and third exons of the gene). Both forms of mRNA are unstable, with half-lives of ca. 15 min. Both encode the previously identified 65,000 and 67,000-dalton products of NMYC. However, the alternative first exons contain distinctive open reading frames that may diversify the coding potential of NMYC. The complexities in transcription of NMYC expand the means by which expression of the gene might be controlled.

Base Sequence↗

Evolution of gonadotropin deficiency in a patient with type II autosomal dominant GH deficiency.

BACKGROUND: Type II isolated GH deficiency (IGHD type II) is caused by dominant negative splicing or point mutations of the GH-1 gene. Studies have suggested that dominant mutant GH forms prevent the secretion of wild-type GH, resulting in eventual cell death; surprisingly, some patients with these GH mutations develop other hormonal deficiencies (ACTH, TSH). SUBJECTS: The proband presented at the age of 2.3 years with IGHD. His father, also known to have been treated for IGHD as a child, had subsequently been lost to follow-up, having remained without treatment during this time. At re-evaluation at the age of 38 years, he complained of lack of stamina and poor libido. Clinical and biochemical assessment confirmed severe GHD, borderline ACTH insufficiency, suboptimal basal and stimulated gonadotropins, and a poor prolactin response to provocation. The basal testosterone concentration was low, and he complained of secondary infertility. Magnetic resonance imaging revealed anterior pituitary hypoplasia in both patients. Genetic testing revealed a heterozygous splicing mutation in GH-1 (intervening sequence-3 + 1G>A) in both patients, known to cause IGHD type II. INTERVENTIONS: The proband showed an excellent growth response to recombinant human GH (rhGH). His father, also treated with rhGH, showed improved quality of life on rhGH, but testosterone concentrations continued to decline, necessitating treatment with testosterone with symptomatic benefit but no improvement in semen quality. CONCLUSIONS: This case supports recent experimental and clinical observations suggesting that the cytotoxicity associated with accumulation of dominant negative mutant 17.5 kDa GH causes a form of GHD that can evolve into multiple hormone deficiencies. Hence, patients diagnosed initially with IGHD type II require continued long-term clinical follow-up.

Adrenocorticotropic Hormone↗

The complex life of WT1.

The Wilms' tumour gene, WT1, encodes a zinc-finger transcription factor that is inactivated in a subset of Wilms' tumours. Mutation analysis in human patients and genetic experiments in mice have revealed that WT1 has a role much wider than just tumour suppression. Alternative splicing, RNA editing, and the use of alternative translation initiation sites generate a multitude of isoforms, which seem to have overlapping but also distinct functions during embryonic development and the maintenance of organ function. Recently, mouse strains lacking the WT1(-KTS) or WT1(+KTS) splice variants of exon 9 were generated. More severe defects of kidneys and gonads are found in mice lacking the WT1(-KTS) variant. Animals lacking the WT1(+KTS) variant show disturbed podocyte function and male-to-female sex reversal. Alternative splicing of exon 5, however, might not modify WT1 function dramatically. Recently, it was also described that reduction of WT1 levels in the kidney results in glomerulosclerosis and upregulation of WT1 in the heart might contribute to neovascularization after infarction.

Alternative Splicing↗

Cloning, expression, and alternative splicing of neogenin1 in zebrafish.

Caenorhabditis elegans UNC-40, Drosophila Frazzled, and vertebrate Neogenin and DCC constitute a subgroup of the immunoglobulin superfamily (IgSF). They possess four immunoglobulin-like domains and six fibronectin-type III repeats at the extracellular region, a single transmembrane region, and a approximately 300 amino-acid intracellular region. UNC-40, Frazzled and DCC can function in axon guidance as the receptor of Netrin (Cell Mol. Life Sci. 56 (1999) 62; Curr. Opin. Cell Biol. 10 (1998) 609). Neogenin binds to Netrin-1 with the same affinity as DCC in vitro (Cell 87 (1996) 175), and is expressed by neurons as they project axons (J. Cell Biol. 127 (1994) 2009), suggesting that it is also a DCC-like Netrin receptor. A zebrafish homologue of DCC (zDCC) is reported recently (Mech. Dev. 109 (2001) 105), but so far there is no report of zebrafish Neogenin. To elucidate a possible neural function of vertebrate Neogenin, we cloned and characterized a zebrafish homologue of neogenin, zneo1, and identified four alternative splice sites within it. In the adult, despite broad tissue distribution, our reverse transcription polymerase chain reaction and Northern analyses demonstrated the dominant expression of zneo1 mRNA in brain. We detected zneo1 mRNA in the embryos from 10 hpf onward and revealed its spatiotemporally regulated expression pattern in both neuronal and non-neuronal tissues by in situ hybridization. Our data showed that during early brain development, zneo1 mRNA was not only present in the proliferative ventricular zones but also in the domains of several first postmitotic neuron clusters when they extended axons. Alternative splicing generates several isoforms of zneo1. Most of them are developmentally regulated, showing distinct distribution in brain and other tissues.

Alternative Splicing↗

The 3' untranslated region of the membrane-bound IL-1R accessory protein mRNA confers tissue-specific destabilization.

IL-1alpha and IL-1beta are proinflammatory cytokines that promote activation of intracellular signaling cascades, leading to stabilization of certain mRNAs and activation of transcription factors. IL-1R type I (IL-1RI) binds IL-1alpha and IL-1beta, and subsequent recruitment of the membrane-bound IL-1R accessory protein (mIL-1RAcP) facilitates signal transduction. Two alternatively spliced isoforms, soluble IL-1RAcP (sIL-1RAcP) and sIL-1RAcP-beta, which lack transmembrane and intracellular domains, have been described. The sIL-1RAcP and possibly sIL-1RAcP-beta can inhibit IL-1 signaling. Proportional expression of the different IL-1RAcP splice variants may be an important determinant of responsiveness to IL-1. We show that although both mIL-1RAcP and sIL-1RAcP mRNAs are widely expressed in human tissue, their relative proportions differ significantly in a tissue-specific manner. Turnover studies revealed that the sIL-1RAcP mRNA has a half-life of approximately 48 h in both the kidney cell line 293 and the hepatoma cell line HepG2. The mIL-1RAcP mRNA has a similar half-life in 293 cells, but a considerably shorter half-life of approximately 5 h in HepG2 cells. Using luciferase reporter constructs, we demonstrated that this specific destabilization of the mIL-1RAcP mRNA in the latter cell type is mediated by its 2.8-kb 3'-untranslated region. Deletion analysis further established that the cell line-specific instability does not involve AU-rich elements, but is mediated by several novel elements that appear to act independently; such elements may be recognized by proteins expressed specifically in some, but not all, tissues. These data demonstrate that the cellular capacity to respond to IL-1 is tightly regulated in a tissue-specific manner.

3' Untranslated Regions↗

Characterization of Trypanosoma cruzi TcRjl locus and analysis of its transcript.

RJLs represent a recently described family of the Ras-related GTP-binding proteins. The Trypanosoma cruzi orthologue, TeRjl, was isolated and its locus was characterized in a region of almost 5 kb. Its 660 bp orf, predicting a protein of 24.13 kDa, is present as a single copy gene in T. cruzi I lineage, and from 1-2 copies in T. cruzi II lineage. TcRjl shares 73% aa sequence similarity with its closest identified orthologue, T. brucei TbRjl. RT-PCR experiments revealed that TcRjl is transcribed in mRNA in the 3 main life forms of the parasite, while Northern hybridization demonstrated that TcRjl is transcribed in T. cruzi epimastigotes as at least 2 transcripts, one of around 950 nt and the other of 1500 nt. Splice-leader addition was mapped to a single site at -69 bp upstream of TcRjl orf indicating that the two mRNA types may derive in differences at the 3' of TcRjl mRNA. TcRjl locus presents considerable synteny with Rjl loci from Trypanosoma brucei and Leishmania major as available from their respective genome projects.

Amino Acid Sequence↗

IRAK1b, a novel alternative splice variant of interleukin-1 receptor-associated kinase (IRAK), mediates interleukin-1 signaling and has prolonged stability.

Interleukin-1 (IL-1) is a pleiotropic cytokine essential for initiation of the immune response to infections and stress. IL-1 interacts with its type I receptor (IL-1RI) and triggers a number of intracellular signaling cascades leading to activation of transcription factors, transcriptional up-regulation of target genes, and mRNA stabilization. IL-1RI-associated kinase-1 (IRAK1) is a membrane proximal serine-threonine kinase involved in IL-1 signaling that becomes phosphorylated and progressively degraded in response to IL-1 induction. We have identified a novel variant of IRAK1, which we have named IRAK1b, that arises from the use of an alternative 5'-acceptor splice site defined by sequence within exon 12 of IRAK1. IRAK1b mRNA exhibits wide tissue expression and is evolutionarily conserved in both mouse and human. IRAK1b can activate the transcription factor nuclear factor kappaB and interacts with the IL-1 signaling factors Toll-interacting protein and tumor necrosis factor receptor-associated factor 6. It forms homodimers and heterodimers with the previously described isoform of IRAK1. We show that the IRAK1b protein is kinase-inactive and that, unlike IRAK1, its levels remain constant after IL-1 induction. The presence of an alternative splice variant of IRAK1, which is functionally active and highly stable following IL-1 stimulation, adds further complexity to the control mechanisms that govern IL-1 signaling.

Alternative Splicing↗

CCND1 polymorphism and age of onset of hepatoblastoma.

Cyclin D1, encoded by the gene CCND1, is a major regulator of the cell cycle transition from G1 phase to S phase. A CCND1 polymorphism (G to A) at codon 242, the boundary of exon 4 and intron 4, affects splicing such that exon 5 is not expressed in the A allele. Since exon 5 is involved in rapid turnover, the variant cyclin D1 corresponding to the A allele may have a longer half-life. A previous study demonstrated that in families with hereditary nonpolyposis colorectal cancer, the age of onset of colorectal cancer varied according to variation at this polymorphic site. We examined this CCND1polymorphism in a series hepatoblastoma, a childhood liver cancer that shares other molecular features with colon cancer. We determined in an analysis of 84 children with hepatoblastoma that the G/A exon 4 polymorphism in CCND1 is correlated with the age of onset of hepatoblastomas. The A/A genotype is associated with an earlier age of onset compared to the G/A or G/G genotype. The median age of patients with the G/G genotype was 22 months, compared to 17 months in patients with the G/A genotype and 11 months for the A/A genotype. These findings suggest that the CCND1 A polymorphism may contribute to tumor development in children with hepatoblastoma.

Age Distribution↗

Functional copper transport explains neurologic sparing in occipital horn syndrome.

OBJECTIVE: A range of neurologic morbidity characterizes childhood-onset copper transport defects, including severe Menkes disease and milder occipital horn syndrome. Both phenotypes are caused by mutations in ATP7A, which encodes a copper-transporting adenosine triphosphatase, although defects causing occipital horn syndrome are rarely reported and nearly always involve exon-skipping (six of eight prior reports). Our objective was to characterize a novel occipital horn syndrome mutation (N1304S) not associated with aberrant splicing and to determine whether functional copper transport was associated with this allele. METHODS: We studied two brothers with typical occipital horn syndrome and used yeast complementation and timed growth assays, exploiting a Saccharomyces cerevisiae mutant strain, to assess in vitro N1304S copper transport. RESULTS: We documented that N1304S has approximately 33% residual copper transport, a result not inconsistent with a similar patient we reported with an exon-skipping mutation whose cells showed correctly spliced mRNA transcripts 36% of normal. CONCLUSION: These patients' mild neurologic phenotypes, together with our yeast complementation and growth experiments, imply that N1304S does not completely block copper transport to the developing brain early in life. The findings suggest that neurologic sparing in untreated occipital horn syndrome is associated with approximately 30% residual functional activity of ATP7A.

Adenosine Triphosphatases↗

Ubiquitination and degradation of ATF2 are dimerization dependent.

Ubiquitination and proteasome-dependent degradation are key determinants of the half-lives of many transcription factors. Homo- or heterodimerization of basic region-leucine zipper (bZIP) transcription factors is required for their transcriptional activities. Here we show that activating transcription factor 2 (ATF2) heterodimerization with specific bZIP proteins is an important determinant of the ubiquitination and proteasome-dependent degradation of ATF2. Depletion of c-Jun as one of the ATF2 heterodimer partners from the targeting proteins decreased the efficiency of ATF2 ubiquitination in vitro, whereas the addition of exogenously purified c-Jun restored it. Similarly, overexpression of c-Jun in 293T human embryo kidney cells increased ATF2 ubiquitination in vivo and reduced its half-life in a dose-dependent manner. Mutations of ATF2 that disrupt its dimerization inhibited ATF2 ubiquitination in vitro and in vivo. Conversely, removal of residues 150 to 248, as in a constitutively active ATF2 spliced form, enhanced ATF2 dimerization and transactivation, which coincided with increased ubiquitination and decreased stability. Our findings indicate the increased sensitivity of transcriptionally active dimers of ATF2 to ubiquitination and proteasome-dependent degradation. Based on these observations, we conclude that increased targeting of a transcriptionally active ATF2 form indicates the mechanism by which the magnitude and the duration of the cellular stress response are regulated.

Activating Transcription Factor 2↗

5'-heterogeneity of glucocorticoid receptor messenger RNA is tissue specific: differential regulation of variant transcripts by early-life events.

Glucocorticoid receptor (GR) gene expression is regulated in a complex tissue-specific manner, notably by early-life environmental events that program tissue GR levels. We have identified and characterized several new rat GR mRNAs. All encode a common protein, but differ in their 5'-leader sequences as a consequence of alternate splicing of, potentially, 11 different exon 1 sequences. Most are located in a 3-kb CpG island, upstream of exon 2, that exhibits substantial promoter activity in transfected cells. Ribonuclease (RNase) protection analysis demonstrated significant levels of six alternate exons 1 in vivo in rat, with differences between liver, hippocampus, and thymus reflecting tissue-specific differences in promoter activity. Two of the alternate exons 1 (exons 1(6) and 1(10)) were expressed in all tissues examined, together present in 77-87% of total GR mRNA. The remaining GR transcripts contained tissue-specific alternate first exons. Importantly, tissue-specific first exon usage was altered by perinatal environmental manipulations. Postnatal handling, which permanently increases GR in the hippocampus, causing attenuation of stress responses, selectively elevated GR mRNA containing the hippocampus-specific exon 1(7). Prenatal glucocorticoid exposure, which increases hepatic GR expression and produces adult hyperglycemia, decreased the proportion of hepatic GR mRNA containing the predominant exon 1(10), suggesting an increase in a minor exon 1 variant. Such tissue specificity of promoter usage allows differential GR regulation and programming.

Alternative Splicing↗