Molecular cloning and characterisation of the Magang goose prolactin gene

In studying the roles of prolactin in regulation of seasonal reproduction, incubation, broodiness and laying performance in goose, the goose PRL gene was cloned in Magang goose. The goose PRL cDNA shared 98.4%, 92.2%, 92%, and 91.9% sequence homology to duck, turkey, chicken and quail PRLs, respectively. The goose PRL gene consisted of 5 exons and 4 introns, just as in other species. The 5' proximal regulatory region shared high homology with those in other avian species as well, and, apart from other non-specific transcription factor binding sites, contained 2 regulatory element binding sites, a Pit-1 (-130/-122) and a VIP response element (-64/-53). The deduced 199-residue mature goose PRL shared 98.5%, 94%, 93%, and 92% homology to duck, quail, chicken, and turkey PRLs, respectively. When compared with other vertebrates, all residues were found to be highly conserved at the key positions in the 4 conserved domains (PD1-PD4), including the 6 cysteine residues at positions 4, 11, 58, 175, 191, and 199. The only exception was a substitution of Arginine by Histidine at position 176 in the mature PRL peptide. These findings render goose PRL as having a similar hydropathy profile and similar secondary and tertiary structures with other PRLs. Goose PRL also possesses an N-linked glycosylation site (Asn-X-Ser), at position 6, and an alternative glycosylation site (Asn-Gly-Cys), at position 56. Five PRL isoforms were detected in goose, as well as in chicken pituitary glands, by immunoblotting analysis. Results of this study not only provided a starting point for further study of PRL function, synthesis, and secretion in goose species, but also for breeding new goose lines efficiently using the genomic information.

Isolation of recombinant type 2 vaccine-derived poliovirus (VDPV) from a Nigerian child

A type 2 vaccine-derived poliovirus (VDPV), differing from Sabin 2 at 2.5% (22/903) of VP1 nucleotide (nt) positions, was isolated from an incompletely immunized 21-month-old Nigerian child who developed acute flaccid paralysis in 2002. Sequences upstream of nt position 620 (within the 5'-untranslated region [5'-UTR]) and downstream of nt position 5840 (in the 3C(pro) region) were derived from species C enteroviruses unrelated to the oral poliovirus vaccine (OPV) strains. The two substitutions associated with the attenuated phenotype had either recombined out (A(481)-->G in the 5'-UTR) or reverted (Ile(143)-->Thr in VP1). The VDPV isolate had lost the temperature sensitive phenotype of Sabin 2 and it was antigenically distinct from the parental OPV strain, having amino acid substitutions in or near neutralizing antigenic sites 1 and 3. The date of the initiating OPV dose, calculated from the number of synonymous substitutions in the capsid region, was estimated to be approximately 16 to 18 months before onset of paralysis, a finding inconsistent with the most recent mass OPV campaign (conducted 12 days before onset of paralysis) as being the source of infection. Although no related type 2 VDPVs were detected in Nigeria or elsewhere, the VDPV was found in an area where conditions favor VDPV emergence and spread.

Regional rearrangements in chromosome 15q21 cause formation of cryptic promoters for the CYP19 (aromatase) gene

Production of appropriate quantities of estrogen in various tissues is essential for human physiology. A single gene (CYP19), regulated via tissue-specific promoters, encodes the enzyme aromatase, which catalyzes the key step in estrogen biosynthesis. Aromatase excess syndrome is inherited as autosomal dominant and characterized by high systemic estrogen levels, short stature, prepubertal gynecomastia and testicular failure in males, and premature breast development and uterine pathology in females. The underlying genetic mechanism is poorly understood. Here, we characterize five distinct heterozygous rearrangements responsible for aromatase excess syndrome in three unrelated families and two individuals (nine patients). The constitutively active promoter of one of five ubiquitously expressed genes located within the 11.2 Mb region telomeric to the CYP19 gene in chromosome 15q21 cryptically upregulated aromatase expression in several tissues. Four distinct inversions reversed the transcriptional direction of the promoter of a gene (CGNL1, TMOD3, MAPK6 or TLN2), placing it upstream of the CYP19 coding region in the opposite strand, whereas a deletion moved the promoter of a fifth gene (DMXL2), normally transcribed from the same strand, closer to CYP19. The proximal breakpoints of inversions were located 17-185 kb upstream of the CYP19 coding region. Sequences at the breakpoints suggested that the inversions were caused by intrachromosomal nonhomologous recombination. Splicing the untranslated exon downstream of each promoter onto the identical junction upstream of the translation initiation site created CYP19 mRNA encoding functional aromatase protein. Taken together, small rearrangements may create cryptic promoters that direct inappropriate transcription of CYP19 or other critical genes.

Full-length sequence analysis of four IBDV strains with different pathogenicities

Characterization of field isolate 9109, Lukert, Edgar cell culture-adapted (CCA), and Edgar chicken embryo-adapted (CEA) serotype 1 IBDV strains using full-length genomic sequences is reported. IBDV genomic segments A and B were sequenced and the nucleotide and deduced amino acid (aa) sequences were compared with previously reported full-length sequenced IBDV strains. We found that the viral protein VPX and amino acid sequences between aa 202-451 and 210-473 of VP2 but not the entire VP2 protein are the best representatives of the entire IBDV genome. The greatest variability was found in the VP2 and 5' non-coding region of segment B among IBDV strains. The deduced amino acid sequences of the VP1 protein varies in length among the strains analyzed. The RNA-dependent, RNA-polymerase motifs within VP1 and the VP5 protein were highly conserved among isolates. Although within the VP2 processing site, amino acid sequence of Lukert was similar to the classical while the Edgar CCA, and CEA were more similar to the very virulent strains, it was determined that these strains have sequence characteristics of the classical strains. In addition, close relatedness between Lukert, Edgar CCA and CEA was observed. Although phylogenetic analysis of the VP1, VP3, and VP4 proteins indicated that 9109 is a classical type virus, this isolate shares unique amino acid changes with very virulent strains within the same proteins. Phylogenetic analysis of the 3' and 5' non-coding regions of segment A revealed that 9109 is more similar to the very virulent strains compared to the classical strains. In the VP2 protein, several amino acids were conserved between variant E and 9109 strains. Thus, it appears that 9109 isolate has characteristics of classical, very virulent, and variant strains. Our analysis indicates that although VPX amino acid comparison may be initially useful for molecular typing, full-length genomic sequence analysis is essential for thorough molecular characterization as partial sequences may not designate a particular strain as very virulent, classical, or variant.

Robust analysis of 5'-transcript ends: a high-throughput protocol for characterization of sequence diversity of transcription start sites

The structure and diversity at the 3' ends of mRNA transcripts have been extensively characterized using several tag-based techniques in eukaryotes. However, the 5' ends of mRNA transcripts are not well understood, owing to a lack of efficient experimental approaches. We developed a new gene expression profiling method, called robust analysis of 5'-transcript ends (5' RATE), to rapidly isolate the 5' ends of mRNA transcripts. After ligating RNA oligo linkers to the 5' regions of decapped mRNA, cDNA is synthesized and digested with the restriction enzyme NlaIII. Ditags are formed by ligating two individual NlaIII tags, and are then PCR-amplified, purified and sequenced using a pyrosequencing approach. The 5'-RATE procedure is simple, fast and cost-effective because the complicated steps in comparative methods such as serial analysis of gene expression (including the formation of concatemers and their subsequent cloning and sequencing) have been eliminated. The longer 5'-RATE tags (>80 bp) provide more accurate matching to reference sequences for gene annotation and allow in-depth analysis of sequence diversity at the 5' regions of mRNA transcripts. Using our procedure, a 5'-RATE library with about 180,000 end sequences can be generated within a week. We have successfully applied the 5'-RATE method to characterize the transcriptome of various plant species including maize, rice and soybean. This method can be easily adapted to other eukaryotic organisms using the detailed procedures described in this protocol.

Intron Size, Abundance, and Distribution within Untranslated Regions of Genes

Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species, Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5' UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5' UTRs than in CDSs. Introns in 5' UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5' UTR-CDS boundary. We propose a mechanistic explanation for the existence of selection for larger intron size in 5' UTRs, and outline several implications of this hypothesis. We found introns to be randomly distributed within 5' UTRs, so long as a minimum required exon size was assumed. Introns in 3' UTRs were much less abundant than in 5' UTRs. Though this was expected for human and mouse that have intron-dependent nonsense-mediated decay (NMD) pathways that discourage the presence of introns within the 3' UTR, it was also true for A. thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general.

Investigation into a school enterovirus outbreak using PCR detection and serotype identification based on the 5' non-coding region

A summer camp was followed by an outbreak of illness involving around 90 children. Investigations included individual questionnaires, inspection of the camp facilities, and laboratory analysis of water and clinical samples. Contamination of drinking and swimming water was demonstrated. An enterovirus was detected by polymerase chain reaction (PCR) and/or culture in 4/4 cerebrospinal fluid samples, 9/15 (60%) stool samples from symptomatic children and 2/9 (22%) stool samples from asymptomatic children. The virus was identified as an echovirus 3 by sequencing and phylogenetic analysis of a short 5' non-coding region (NCR) PCR product. Viruses from the outbreak clustered closely and an echovirus 3 from a temporally associated non-outbreak case could be readily distinguished. Despite the lack of a standardized approach, direct molecular detection and identification of enteroviruses is an efficient epidemiological tool. Here the 5'-NCR was successfully used for both detection and 'serotyping', and the close genetic relatedness of isolates was proven.

Use of armored RNA as a standard to construct a calibration curve for real-time RT-PCR

Armored Enterovirus RNA was used to standardize a real-time reverse transcription (RT)-PCR for environmental testing. Armored technology is a system to produce a robust and stable RNA standard, trapped into phage proteins, to be used as internal control. The Armored Enterovirus RNA protected sequence includes 263 bp of highly conserved sequences in 5' UTR region. During these tests, Armored RNA has been used to produce a calibration curve, comparing three different fluorogenic chemistry: TaqMan system, Syber Green I and Lux-primers. The effective evaluation of three amplifying commercial reagent kits, in use to carry out real-time RT-PCR, and several extraction procedures of protected viral RNA have been carried out. The highest Armored RNA recovery was obtained by heat treatment while chemical extraction may decrease the quantity of RNA. The best sensitivity and specificity was obtained using the Syber Green I technique since it is a reproducible test, easy to use and the cheapest one. TaqMan and Lux-primer assays provide good RT-PCR efficiency in relationship to the several extraction methods used, since labelled probe or primer request in these chemistry strategies, increases the cost of testing.

Alternative usages of multiple promoters of the acetyl-CoA carboxylase beta gene are related to differential transcriptional regulation in human and rodent tissues

Acetyl-CoA carboxylase beta (ACCbeta) is a critical enzyme in the regulation of fatty acid oxidation and is dominantly expressed in the skeletal muscle, heart, and liver. It has been established that two promoters, P-I and P-II, control the transcription of the ACCbeta gene. However, the precise mechanism involved in controlling tissue-specific gene expression of ACCbeta is largely unknown yet. In this study we revealed that promoter P-I, active in the skeletal muscle and heart but not in the liver, could be activated by myogenic regulatory factors and retinoid X receptors in a synergistic manner. Moreover, P-I was also activated markedly by the cardiac-specific transcription factors, Csx/Nkx2.5 and GATA4. These results suggest that the proper stimulation of P-I by these tissue-specific transcription factors is important for the expression of ACCbeta according to the tissue types. In addition, CpG sites around human exon 1a transcribed by P-I are half-methylated in muscle but completely methylated in the liver, where P-I is absolutely inactive. In humans, the skeletal muscle uses P-II as well as P-I, whereas only P-I is active in rat skeletal muscle. The proximal myogenic regulatory factor-binding sites in human P-II, which are not conserved in rat P-II, might contribute to this difference in P-II usage between human and rat skeletal muscle. Hepatoma-derived cell lines primarily use another novel promoter located about 3 kilobases upstream of P-I, designated as P-O. This study is the first to explain the mechanisms underlying the differential regulation of ACCbeta gene expression between tissues in living organisms.

Evaluation of a prototype HCV NS5b assay for typing strains of hepatitis C virus isolated from Tunisian haemodialysis patients

Hepatitis C virus (HCV) strains isolated from 68 haemodialysis Tunisian patients exhibiting chronic infection were genotyped targeting the NS5b region of the HCV genome using a prototype assay developed by Bayer HealthCare-Diagnostics (TRUGENE NS5b HCV). The overall results were compared to those obtained with another assay of the same company based on sequencing of the 5' non-coding region (TRUGENE HCV 5'NC genotyping kit). All strains could be typed by the 5'NC typing kit, but only 62 (91; 2%) by the NS5b prototype assay. All the 62 strains typed by both methods exhibited the same pattern at the type level: 57 were type 1, 3 were type 2, and 2 were type 4. At the subtype level, eight strains that gave undetermined results by the 5'NC kit were successfully typed by the NS5b kit; eight additional strains exhibited discrepant results. The overall agreement between the two assays was 74.2% at the subtype level. In conclusion, the NS5b region appears to be much more accurate than the 5'NC region to subtype HCV strains, especially in those isolated from patients attending haemodialysis centres where the subtype distribution suggests frequent nosocomial transmissions.

Human CD94 gene expression: dual promoters differing in responsiveness to IL-2 or IL-15

CD94 is a C-type lectin required for the dimerization of the CD94/NKG2 family of receptors, which are expressed on NK cells and T cell subsets. Little is known about CD94 gene expression and the elements that regulate CD94 transcription. In this study, we report that CD94 gene expression is regulated by distal and proximal promoters that transcribe unique initial exons specific to each promoter. This results in two species of transcripts; the previously described CD94 mRNA and a novel CD94C mRNA. All NK cells and CD94(+), CD8(+) alphabeta T cells transcribe CD94 mRNA. Stimulation of NK and CD8(+) alphabeta T cells with IL-2 or IL-15 induced the transcription of CD94C mRNA. The distal and proximal promoters both contain elements with IFN-gamma-activated and Ets binding sites, known as GAS/EBS. Additionally, an unknown element, termed site A, was identified in the proximal promoter. EMSA analyses showed that constitutive factors could bind to oligonucleotide probes containing each element. After treatment of primary NK cells with IL-2 or IL-15, separate inducible complexes could be detected with oligonucleotide probes containing either the proximal or distal GAS/EBS elements. These elements are highly conserved between mice and humans, which suggests that both species regulate CD94 gene expression via mechanisms that predate their evolutionary divergence.

Real-time PCR for rapid diagnosis of entero- and rhinovirus infections using LightCycler

BACKGROUND

PCR techniques have proved to be more sensitive than traditional cell culture in the diagnosis of enterovirus and rhinovirus infections and are widely used in clinical virus laboratories. However, PCR assays are relatively time-consuming and labor intensive, particularly if separate hybridization steps are used to confirm the specificity of positive findings.

OBJECTIVES

The aim of the present study was to develop fast and sensitive real-time PCR assay, which would allow simultaneous detection of entero- and rhinoviruses and their quantification in clinical and experimental samples.

STUDY DESIGN

Two real-time RT-PCR protocols were developed using LightCycler (LC) technology; SYBRGreen and hybridization probe assays. The sensitivity of these assays to detect entero- and rhinoviruses was compared with that of a traditional reference RT-PCR-hybridization assay and cell culture. All PCR protocols used the same primers amplifying the 5'-non coding region (NCR) of entero- and rhinoviruses. The LC probe assay and the reference RT-PCR used almost identical detection probes, which bind to enterovirus specific amplicons.

RESULTS AND CONCLUSIONS

Both real-time PCR assays were equally sensitive as the reference RT-PCR-assay and all were more sensitive than cell culture. Both real-time assays quantified reliably the amount of the virus and took much shorter time than the reference RT-PCR. As the real-time SYBRGreen assay detects both entero- and rhinoviruses it can be used for primary screening of samples, which can be positive for either of these viruses. The real-time probe-assay can confirm the presence of enterovirus in SYBRGreen positive samples or it can be used for selective screening of enteroviruses e.g. from CSF samples.

Direct comparison of hepatitis C virus genotypes tested by INNO-LiPA HCV II and TRUGENE HCV genotyping methods

BACKGROUND

Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. It is associated with the development of end-stage liver disease and hepatocellular carcinoma. Studies have shown that patients infected with different genotypes of HCV may respond to interferon-ribavirin therapy differently and thus HCV genotype information is very important in helping physicians to better managing their patients.

OBJECTIVES

Compare the end results of HCV typing of the two commercially available tests.

STUDY DESIGN

TRUGENE Genotyping test (Visible Genetics) was used to analyze clinical specimens obtained from North America. The 5' NC was amplified with the Roche COBAS Amplicor HCV Monitor Test. Amplification products were blinded and genotyped by the TRUGENE HCV 5'NC method. Genotype results were compared with those obtained by the reverse hybridization based INNO-LiPA HCV II (Innogenetics) assay. Additional sequencing of the NS5B region was done to resolve discrepancies.

RESULTS AND CONCLUSIONS

Among the total of 110 consecutively collected serum specimens submitted for HCV genotyping, 108/110 could be typed by the sequencing method and 107/110 were typable by LiPA HCV II method. Our experiences with the tests suggest that at type level, HCV genotype results are 100% concordant between the two tests studied for those 106 specimens successfully typed by both methods. More sensitive amplification, such as qualitative PCR, is needed to test specimens with viral load lower than 20000 IU/ml. Both tests can be easily adapted by a clinical diagnostic laboratory.

Exploring the role of 5' alternative splicing and of the 3'-untranslated region of cathepsin B mRNA

The cysteine peptidase cathepsin B is responsible for connective tissue breakdown in several diseases. The pathological expression of cathepsin B may depend on the structure of its mRNA. We investigated the translational efficiency of the cathepsin B mRNA untranslated regions (UTRs) using fusion constructs to green fluorescent protein (GFP) and luciferase. Transfection of fusion constructs with GFP and luciferase containing the full-length 5'-UTR, the variant lacking exon 2, and that lacking exons 2 and 3 into mammalian cells, resulted in modulation of the biosynthetic rate of cathepsin B in a cell-specific manner. Constructs missing these exons were biosynthetically more efficient than the full-length counterpart. Luciferase was cloned upstream of the 3'-UTR, downstream of the 5'-UTR, or sandwiched between the 5'- and the 3'-UTR. The UTRs of cathepsin B downregulated luciferase biosynthesis moderately when present individually, with the 3'-UTR being more efficient than the 5'-UTR, and downregulated it even more when present simultaneously. A truncated cathepsin B-GFP chimeric product derived from the 5'-UTR missing exons 2 and 3 induced cell death. The increased biosynthetic rate and abnormal trafficking of cathepsin B observed in pathologies such as cancer and osteoarthritis may depend on alternative splicing of pre-mRNA.

Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus

The satellite RNA of Bamboo mosaic virus (satBaMV) contains on open reading frame for a 20-kDa protein that is flanked by a 5'-untranslated region (UTR) of 159 nucleotides (nt) and a 3'-UTR of 129 nt. A secondary structure was predicted for the 5'-UTR of satBaMV RNA, which folds into a large stem-loop (LSL) and a small stem-loop. Enzymatic probing confirmed the existence of LSL (nt 8-138) in the 5'-UTR. The essential cis-acting sequences in the 5'-UTR required for satBaMV RNA replication were determined by deletion and substitution mutagenesis. Their replication efficiencies were analyzed in Nicotiana benthamiana protoplasts and Chenopodium quinoa plants coinoculated with helper BaMV RNA. All deletion mutants abolished the replication of satBaMV RNA, whereas mutations introduced in most of the loop regions and stems showed either no replication or a decreased replication efficiency. Mutations that affected the positive-strand satBaMV RNA accumulation also affected the accumulation of negative-strand RNA; however, the accumulation of genomic and subgenomic RNAs of BaMV were not affected. Moreover, covariation analyses of natural satBaMV variants provide substantial evidence that the secondary structure in the 5'-UTR of satBaMV is necessary for efficient replication.

Characterization and analysis of the proximal Janus kinase 3 promoter

Janus kinase 3 (Jak3) is a nonreceptor tyrosine kinase essential for signaling via cytokine receptors that comprise the common gamma-chain (gammac), i.e., the receptors for IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. Jak3 is preferentially expressed in hemopoietic cells and is up-regulated upon cell differentiation and activation. Despite the importance of Jak3 in lymphoid development and immune function, the mechanisms that govern its expression have not been defined. To gain insight into this issue, we set out to characterize the Jak3 promoter. The 5'-untranslated region of the Jak3 gene is interrupted by a 3515-bp intron. Upstream of this intron and the transcription initiation site, we identified an approximately 1-kb segment that exhibited lymphoid-specific promoter activity and was responsive to TCR signals. Truncation of this fragment revealed that core promoter activity resided in a 267-bp fragment that contains putative Sp-1, AP-1, Ets, Stat, and other binding sites. Mutation of the AP-1 sites significantly diminished, whereas mutation of the Ets sites abolished, the inducibility of the promoter construct. Chromatin immunoprecipitation assays showed that histone acetylation correlates with mRNA expression and that Ets-1/2 binds this region. Thus, transcription factors that bind these sites, especially Ets family members, are likely to be important regulators of Jak3 expression.

Crucial role of DNA methylation in determination of clonally distributed killer cell Ig-like receptor expression patterns in NK cells

Human NK cells are characterized by the expression of surface receptors of the killer cell Ig-like receptor (KIR) family, which are involved in the specific recognition of pathogenic target cells. Each NK cell expresses and maintains an individual subset of inhibitory and stimulatory KIR and in this way contributes to a diversified NK cell repertoire. To date, the molecular basis for generation of clonally distributed KIR expression patterns has been elusive. Here, analyses of DNA methylation patterns of KIR genes in NK cell lines as well as in NK cells, freshly isolated from peripheral blood, demonstrated that a small CpG island surrounding the transcriptional start site of each KIR gene is consistently demethylated in expressed KIR and methylated in unexpressed KIR. DNA-demethylating treatment resulted in a rapid and stable induction of transcription and cell surface expression of all formerly unexpressed KIR in NK cell lines, NK cell clones, and freshly isolated NK cells, but not in other cell types. In vitro methylation of KIR CpG islands repressed reporter gene expression in NK cells. We conclude that clonal patterns of KIR expression are mainly epigenetically determined and maintained through DNA methylation.

Performance of TRUGENE hepatitis C virus 5' noncoding genotyping kit, a new CLIP sequencing-based assay for hepatitis C virus genotype determination

The performance of the recently developed, standardized direct sequencing assay for hepatitis C virus (HCV) genotyping [TRUGENE HCV 5'-NC (noncoding)] was assessed in comparison with the reverse hybridization-based assay INNO-LIPA HCV II. Both assays allow HCV genotyping starting from amplification products generated by the diagnostic Roche AMPLICOR HCV test. HCV amplicons from 205 patients were used for this study: 34 were tested prospectively by both methods, while 171 had been stored at -20 degrees C for up to 2 years after LiPA genotyping. The TRUGENE procedure failed to determine a genotype in six low-titered samples (3.5 +/- 0.3 log UI/mL vs. 5.2 +/- 0.5 UI/mL for typable samples). Type and subtype could be determined by sequencing for 199 samples (97%). Among them, five were considered as coinfections by the LiPA method. Three LiPA patterns suggesting type 1 and 4 coinfection were not supported by sequence analysis while one 1a/2b and one 1a/3a coinfection was backed up by direct sequencing. For the remaining 194 samples, type assignment was concordant in 100% of the cases. LiPA subtyping was available for 162 samples (83.5%). Sub-typing results concurred in 128 cases (79%). NS5B sequencing of discrepant samples underscored the limitation of the 5'-noncoding region (NCR) in correct subtype assignment. In conclusion, the TRUGENE HCV 5'-NC genotyping kit appeared to be a specific and reliable method that can be used in the current indication of HCV genotyping.

Distinct proteins encoded by alternative transcripts of the PURG gene, located contrapodal to WRN on chromosome 8, determined by differential termination/polyadenylation

A gene encoding a new member of the Pur protein family, Purgamma, has been detected upstream of, and contrapodal to, the gene encoding the Werner syndrome helicase, Wrn, at human chromosome band 8p11-12. Both the PURG and WRN genes initiate transcription at multiple sites, the major clusters of which are approximately 90 bp apart. A segment containing this region strongly promotes transcription of a reporter gene in both directions. Both promoters are TATA-less and CAAT-less and both are positively regulated by Sp1 elements. While promoter elements for the two genes are interleaved, in the contrapodal direction, certain elements critical for each gene are distinct. Sequencing of cDNAs for Purgamma mRNA reveals that two alternative coding sequences are generated from a single gene, resulting in different Purgamma C-termini. PURG-A mRNA consists of a single intronless transcript of approximately 3 kb. PURG-B mRNA results from transcription through the PURG-A polyadenylation site and splicing out of an intron of >30 kb. In this unique example of a switch, splicing of a single intron either occurs or does not occur depending upon differential termination/polyadenylation. PURG-B is the primary PURG transcript detected in testis, but it is undetectable in all members of a normal adult tissue cDNA panel. PURG-A levels are low or undetectable in the normal tissue panel, but they are greatly elevated in all members of a tumor tissue panel. PURG-B is detected in several tumor panel members.

Induction of rat organic anion transporting polypeptide 2 by pregnenolone-16alpha-carbonitrile is via interaction with pregnane X receptor

The rat organic anion transporting polypeptide 2 (oatp2; Slc21a5) is a liver transporter that mediates the uptake of a variety of structurally diverse compounds, and has a high affinity for cardiac glycosides. Treatment of rats with pregnenolone-16alpha-carbonitrile (PCN), a ligand for the rodent pregnane X receptor (PXR), significantly enhances the rat oatp2 gene expression. To understand the molecular mechanism of oatp2 induction by PCN, rat oatp2 gene was cloned. The rat oatp2 gene consists of 16 exons; alternative splicing of the second noncoding exon gives rise to the two published rat oatp2 cDNAs. Approximately 8700 base pairs (bp) of the 5'-flanking region of the rat oatp2 gene were linked to the luciferase reporter gene and used in transient transfection assays in H4IIE cells. Treatment of PCN induced the expression of the reporter gene in a dose-dependent manner. Four potential PXR response elements (PXREs) were identified in the 5'-flanking region of the rat oatp2 gene. One element (DR3-1) is located approximately -5000 bp with three more (DR3-2, DR3-3, and DR3-4) clustered at about -8000 bp. Results from electrophoretic mobility shift assays showed that the PXR-retinoid X receptor alpha heterodimer binds to the DR3-2 with the highest affinity, to the DR3-4 and DR3-1 with a lower affinity, and weakly or not at all to the DR3-3. Furthermore, a series of partial deletions of the 5'-flanking region illustrated that both the proximal and distal clusters of PXREs are required for maximal induction of rat oatp2 by PCN. In conclusion, these data elucidate the molecular mechanism by which PCN treatment induces rat oatp2 gene expression. In addition, this study identifies rat oatp2 as a direct PXR-targeted gene and further supports the hypothesis that activation of PXR affects a network of genes that is involved in either metabolism or transport of drugs, steroids, and bile acids.

[Comparative morphological and gene systematics analysis of the Proteocephalus thymalli (Cestoda: Proteocephalidae), a parasite of graylings in lakes Hovsogol and Baikal]

Results of comparative morphological and gene analyses of the cestode Proteocephalus thymalli, an intestine parasite of the lakes Hovsogol (Thymallus arcticus nigrescens) and Lake Baikal graylings (Thymallus arcticus baicalensis) are presented for the first time. The results indicate that representatives of the P. thymalli from these fishes are really two different species.

Cloning of the rat IL-5Ralpha gene: analysis of 5'-upstream region and expression by B cells

Although rats are widely used for the analysis of allergic reactions and parasitic infections where IL-5 is involved, nothing is currently known of the expression of IL-5 receptor in this species. In this study, the cDNA sequence, genomic structure and the transcriptional regulation of the rat IL-5Ralpha were analyzed. The rat IL-5Ralpha gene, which we localized to chromosome 4q34-q41, spans more than 25 kb and consists of 12 exons. Promoter activity was seen in different cell lines and analysis by deletion experiments allowed to identify two negative regulatory regions which did not differ when tested either with IL-5Ralpha-negative or positive cells. Finally, the investigation of the expression of IL-5Ralpha showed that it is expressed in lung, spleen, liver, and purified rat B cells from normal rat. This can provide an explanation for the role of rat IL-5 as B-cell growth factor and a relevant model in order to better understand the activity of IL-5 on human B cells.

A 5' Leader of Rbm3, a Cold Stress-induced mRNA, Mediates Internal Initiation of Translation with Increased Efficiency under Conditions of Mild Hypothermia

Although mild hypothermia generally reduces protein synthesis in mammalian cells, the expression of a small number of proteins, including Rbm3, is induced under these conditions. In this study, we identify an Rbm3 mRNA with a complex 5' leader sequence containing multiple upstream open reading frames. Although these are potentially inhibitory to translation, monocistronic reporter mRNAs containing this leader were translated relatively efficiently. In addition, when tested in the intercistronic region of dicistronic mRNAs, this leader dramatically enhanced second cistron translation, both in transfected cells and in cell-free lysates, suggesting that the Rbm3 leader mediates cap-independent translation via an internal ribosome entry site (IRES). Inasmuch as Rbm3 mRNA and protein levels are both increased in cells exposed to mild hypothermia, the activity of this IRES was evaluated at a cooler temperature. Compared to 37 degrees C, IRES activity at 33 degrees C was enhanced up to 5-fold depending on the cell line. Moderate enhancements also occurred with constructs containing other viral and cellular IRESes. These effects of mild hypothermia on translation were not caused by decreased cell growth, as similar effects were not observed when cells were serum starved. The results suggest that cap-independent mechanisms may facilitate the translation of particular mRNAs during mild hypothermia.

Telomerase activity and expression of telomerase reverse transcriptase correlated with cell proliferation in meningiomas and malignant brain tumors in vivo

Telomerase activity was examined in intracranial tumors and compared with gene expression of the two core components of telomerase--the reverse transcriptase subunit (hTERT) and the RNA subunit (hTR)--and the proliferative index. We investigated 32 tumors across three to five sampled regions (20 meningiomas, 1 acoustic schwannoma, 1 pituitary adenoma, 8 gliomas, and 2 medulloblastomas). Telomerase activity was demonstrated by the telomeric repeat amplification protocol (TRAP) assay in seven (22%) intracranial tumors (four malignant brain tumors, two atypical meningiomas and one ependymoma) but could not be detected in the 18 (100%) benign meningiomas. hTERT and hTR mRNA were detected using reverse-transcription polymerase chain reaction (RT-PCR). hTERT mRNA was present in 20 (63%) intracranial tumors. Whereas hTERT mRNA transcripts were consistently low or absent in meningiomas, malignant brain tumors exhibited elevated hTERT mRNAs. Multiple regions of glioblastomas showed differences in telomerase activity and in the presence of hTERT mRNA. RT-PCR analysis revealed, for the first time in intracranial tumors, the presence of hTERT mRNA spliced products, corresponding to full-length mRNA as well as spliced mRNAs with critical reverse transcriptase motifs deleted. Only tumors with marked telomerase activity showed all hTERT spliced messages simultaneously. The absence of a positive correlation between telomerase activity and hTERT mRNA could not be attributed to the presence of hTERT spliced variants. We found a significant correlation between telomerase activity scores and Ki-67 proliferation index. A positive association is also seen between Ki-67 staining and the degree of hTERT mRNA expression. This shows that there seems to be a relationship between telomerase activity or the degree of hTERT expression and proliferation rate in intracranial tumors.

Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum

We mapped transcription start sites for ten unrelated protein-encoding Pyrobaculum aerophilum genes by primer extension and S(1) nuclease mapping. All of the mapped transcripts start at the computationally predicted translation start codons, two of which were supported by N-terminal protein sequencing. A whole genome computational analysis of the regions from -50 to +50 nt around the predicted translation starts codons revealed a clear upstream pattern matching the consensus sequence of the archaeal TATA box located unusually close to the translation starts. For genes with the TATA boxes that best matched the consensus sequence, the distance between the TATA box and the translation start codon appears to be shorter than 30 nt. Two other promoter elements distinguished were also found unusually close to the translation start codons: a transcription initiator element with significant elevation of C and T frequencies at the -1 position and a BRE element with more frequent A bases at position -29 to -32 (counting from the translation start site). We also show that one of the mapped genes is transcribed as the first gene of an operon. For a set of genes likely to be internal in operons the upstream signal extracted by computer analysis was a Shine-Dalgarno pattern matching the complementary sequence of P. aerophilum 16 S rRNA. Together these results suggest that the translation of proteins encoded by single genes or genes that are first in operons in the hyperthermophilic crenarchaeon P. aerophilum proceeds mostly, if not exclusively, through leaderless transcripts. Internal genes in operons are likely to undergo translation via a mechanism that is facilitated by ribosome binding to the Shine-Dalgarno sequence.

Molecular dissection of hepatitis C virus expression

OBJECTIVE

The 5' untranslated region (5' UTR) of the hepatitis C virus genome is thought to be important for the control of viral gene expression and a likely target for therapeutic interception. A functional role of this viral gene segment was analyzed both in vivo and in vitro.

METHODS

Transgenic mice carrying a reporter gene that contains the complete 5' UTR sequence were made. Cellular protein(s) which associate with the 5' UTR were analyzed by gel shift analysis and a following affinity purification.

RESULTS

Transgenic mice revealed protein accumulation only in periportal hepatocytes around the portal triad and not in perivenous hepatocytes around the central vein. Gel shift analysis using mouse liver extracts provides further evidence that trans-acting proteins, which recognize a specific cis-acting element with the 5' UTR (an apparent stemmed structure formed by two noncontiguous RNA sequences), are present in adult mice but not in young mice. A similar 5' UTR RNA-protein complex was also detected with human liver extracts.

CONCLUSION

The presence of cellular factor(s) which allow HCV 5' UTR to express in tissue and differentiation state-specific manner was suggested.

Positive and negative roles of the trans-acting T cell factor-1 for the acquisition of distinct Ly-49 MHC class I receptors by NK cells

Members of the Ly-49 gene family code for class I MHC-specific receptors that regulate NK cell function. Due to a combinatorial distribution of Ly-49 receptors, NK cells display considerable clonal heterogeneity. The acquisition of one Ly-49 receptor, Ly-49A is strictly dependent on the transcriptional trans-acting factor T cell-specific factor-1 (TCF-1). Indeed, TCF-1 binds to two sites in the Ly-49a promoter and regulates its activity, suggesting that the Ly-49a gene is a direct TCF-1 target. TCF-1 deficiency resulted in the altered usage of additional Ly-49 receptors. We show in this study, using TCF-1 beta(2)-microglobulin double-deficient mice, that these repertoire alterations are not due to Ly-49/MHC class I interactions. Our findings rather suggest a TCF-1-dependent, cell autonomous effect on the acquisition of multiple Ly-49 receptors. Besides reduced receptor usage (Ly-49A and D), we also observed no effect (Ly-49C) and significantly expanded (Ly-49G and I) receptor usage in the absence of TCF-1. These effects did not in all cases correlate with the presence of TCF binding sites in the respective proximal promoter. Therefore, besides TCF-1 binding to the proximal promoter, Ly-49 acquisition may also be regulated by TCF-1 binding to more distant cis-acting elements and/or by regulating the expression of additional trans-acting factors. Consistent with the observed differential, positive or negative role of TCF-1 for Ly-49 receptor acquisition, reporter gene assays revealed the presence of an inducing as well as a repressing TCF site in certain proximal Ly-49 promoters. These findings reveal an important role of TCF-1 for the formation of the NK cell receptor repertoire.

Mitochondrial control region structure and single site heteroplasmy in the razorbill (Alca torda; Aves)

The primary structure of the Alca torda mitochondrial control region was determined and conserved structural features were identified based on sequence comparisons to other bird species. In a population survey using control region analysis, five individuals were found to possess heteroplasmic point mutations at the variable 5' end of the control region. The pattern of variable nucleotide positions among individuals was compared to the distribution of heteroplasmic sites and the heteroplasmic condition was further characterised by a cloning procedure applied to two individuals which harboured one and two heteroplasmic point mutations, respectively. These results are in support of recent evidence that single site heteroplasmy may be more common than previously thought.

Leptin receptor 5'untranslated regions in the rat: relative abundance, genomic organization and relation to putative response elements

Hypothalamic sensitivity to leptin has been suggested to be important for regulation of body fat mass. Mice heterozygous for a mutation in the leptin receptor (leptin-R) have an increased body fat mass suggesting that the abundance of leptin-R may be an important determinator of leptin sensitivity. Leptin-R cDNAs from several species contain alternative 5'untranslated regions (5'UTRs), suggesting that several distinct regulatory regions may exist. To investigate possible mechanisms by which leptin-R expression may be regulated, we searched for possible alternative 5'UTRs of the leptin-R in the rat and determined their location in relation to putative response elements. Four leptin-R 5'UTRs (exons 1A-1D), which diverged 23 bp upstream of the start codon, were identified by 5'Rapid Amplification of cDNA Ends (5'RACE) and sequencing. Exons 1B and 1C were present in 31 and 61%, respectively, of all leptin-R transcripts in the hypothalamus as determined by a ribonuclease protection assay. Analysis of the 5' flanking genomic sequences revealed an imperfect estrogen response element (ERE), two Spl-sites, three CCAAT-boxes and one octamer. Exons 1A and 1D corresponded to a putative second gene, encoding the OB-Receptor Gene Related Protein (OB-RGRP), which is transcribed from a promoter shared with the leptin-R. DNA sequencing revealed that the rat OB-RGRP had 98 and 97% homology with the mouse and human sequence, respectively. We report here that transcription of the rat leptin-R gene may generate transcripts with four alternative 5'UTRs. The presence of a putative ERE, close to the most frequently used transcriptional start sites of the leptin-R gene in the hypothalamus, provides a possible mechanism by which estrogen may exert its effects on food intake.

Organization of ribosomal RNA genes from a Loofah witches' broom phytoplasma

Using the technique of integrative mapping with three vectors carrying chromosomal rDNA sequences, one of two rRNA operons of loofah witches' broom (LfWB) phytoplasma was constructed. This is the first complete rRNA operon of a phytoplasma to be reported. The operon has a context of 5'-16S-23S-5S-3' with a tRNA(Ile) gene in the ITS and tRNA(Val) and tRNA(Asn) genes downstream from the 5S rRNA gene. Although the other operon has not been cloned, the DNA sequence of a PCR-amplified product shows that it has no tRNA(Ile) gene in the ITS region. The complete nucleotide sequences of 16S, 23S, and 5S rDNA are 1538, 2864, and 113 bp, respectively. Five -10-like sequences, but no -35 sequences, were found within a 494-bp leader region. There was a TG dinucleotide two nucleotides upstream from each -10-like sequence. The existence of a TG dinucleotide at this position has been reported to enhance the efficiency of a promoter without a -35 region. The regions immediately flanking the 5' and 3' ends of 16S and 23S rDNA can form long basepaired stems that contain sites for processing by RNase III. No obvious sequence for a rho-dependent or rho-independent termination site was found downstream from the tRNA(Asn) gene. The transcription may stop within a pyrimidine-rich region, as has been reported for several polypeptide-encoding genes and rRNA operons of archaeobacteria. The presence of the tRNA genes downstream from the 5S rRNA gene in the rRNA operon of LfWB phytoplasma further supports the hypothesis that phytoplasmas are phylogenetically closer to acholeplasmas than to mycoplasmas. The phylogenetic relatedness of LfWB phytoplasma to other phytoplasmas is discussed on the basis of the nucleotide sequence of rRNA genes and ITS.

Homotypic echoviruses share aminoterminal VP1 sequence homology applicable for typing

Molecular typing of enteroviruses should ideally focus on regions encoding determinants for neutralization. Mapping of monoclonal neutralizing antibodies has shown the VPI protein, in particular its aminoterminal part, encompassing the B-C loop, to be one major antigenic region. We therefore sequenced 570 nucleotides from the 5'-end of the VP1 region of the genome for all 28 echovirus prototypes, and for 61 clinical isolates representing all different echovirus types. An analysis of 133 sequences, including 39 sequences retrieved from GenBank, classified all echoviruses in enterovirus group B confirming results from sequencing within the VP2 region. The nucleotide and amino acid divergence of VP1 sequences of homotypic strains varied from 7.5-23.0% and from 0.0-5.3%, respectively, when compared to their corresponding prototypes, whereas strains belonging to different serotypes these divergences were 22.1-38.9 % and 4.9-16.4 %, respectively. Despite these minimal overlaps, the VP1 sequence was always more similar to that of the homotypic prototype than to that of any heterotypic strain. For 13 out of 14 echovirus types, where multiple isolates were available, the corresponding VP1 sequences diverged more from those of the prototype than from the other homotypic sequences as a reflection of genetic drift. Because there was a complete concordance between the sequences of the region encoding the VP1 aminoterminus and the serotype (P< 0.00001) sequence analysis of this region might complement typing by neutralization, and classify correctly echovirus isolates that may not be typed conveniently by the antisera in hand.

The error-prone DNA polymerase zeta catalytic subunit (Rev3) gene is ubiquitously expressed in normal and malignant human tissues

Mutagenesis induced by UV light and chemical agents in yeast is largely dependent on the function of Rev3, the catalytic subunit of DNA polymerase zeta that carries out translesion DNA synthesis. Human and mouse homologues of the yeast Rev3 gene have recently been identified, and inhibition of Rev3 expression in cultured human fibroblasts by Rev3 anti-sense was shown to reduce UV-induced mutagenesis, indicating that Rev3 also plays a crucial role in mutagenesis in mammalian cells. A common variant transcript with an insertion of 128-bp between nucleotides +139 and +140 is found in both human and mouse Rev3 cDNAs, but its biological significance has not been defined. We show here that the insertion variant is not translatable either under in vitro or in vivo conditions. We also found that the translational efficiency of Rev3 gene is enhanced by the 5' untranslated region that contains a putative stem-loop structure postulated to inhibit the translation. Since the human Rev3 gene is localized to chromosome 6q21, a region previously shown to contain genes involved in tumor suppression and cellular senescence, we examined its expression in various normal and malignant tissues. Rev3 and its insertion variant transcripts were ubiquitously detected in all 27 normal human tissues studied, with an additional variant species found in tissues with relatively high levels of Rev3 expression. Levels of Rev3 transcripts were similar in lung, gastric, colon and renal tumors compared to normal tissue counterparts. The data indicate that Rev3 expression is ubiquitous and is not dysregulated in malignancies.

Cloning of the mouse Pax4 gene promoter and identification of a pancreatic beta cell specific enhancer

Pax4 encodes a paired-box transcription factor and is essential for the differentiation of islet cells since the Pax4 homozygous mutant mice lack mature beta and delta cells. However, little is known about the transcriptional regulation of the Pax4 gene. We isolated and sequenced a 2.4-kb mouse genomic DNA fragment containing the 5' flanking sequence of Pax4 and identified a previously unrecognized intron. Primer extension revealed that this TATA-less promoter had only one transcription start site. The promoter activity of this fragment with various deletion mutants when tested in beta and non-beta cell lines indicated the presence of a beta-cell specific enhancer in the region, -1858 to -1954 bp. DNase 1 footprinting and gel retardation assays indicated that nuclear proteins from betaHC3 cells interacted with two sequences which contained putative CdxA/Nkx.2 and GATA-1,-2 binding sites. Site-directed mutagenesis indicated that both of these regions were necessary for beta-cell specific enhancer activity.

Rat protein kinase c zeta gene contains alternative promoters for generation of dual transcripts with 5'-end heterogeneity

Protein kinase C (PKC) zeta is a phospholipid-dependent serine/threonine kinase that appears to perform important cell signaling functions. Two forms of PKC zeta RNA, with different 5' ends, have been reported. The major form (zeta) is expressed in most, if not all tissues, while the minor form (zeta'), which encodes the catalytic domain of the enzyme without most of its regulatory domain, is predominant in normal brain and certain rat prostate tumors. We report here the structure of the 5' end of the rat PKC zeta gene, demonstrating that both forms of RNA can be transcribed from the same gene through the use of alternative promoters and splicing. In luciferase reporter constructs, progressive deletions of the PKC zeta and zeta' 5' flanking sequences yielded activities that were higher in the cell lines expressing endogenous PKC zeta and zeta' RNAs, respectively. Also, multiple PCRs across different introns of the PKC zeta gene indicate that recent duplication of the gene or the existence of a closely related pseudogene in the rat genome are unlikely.

5'-UTR structural organization, transcript expression, and mutational analysis of the human Rab geranylgeranyl transferase alpha-subunit (RABGGTA) gene

Hermansky-Pudlak syndrome (HPS) is a recessively inherited disease with dysfunction of several related subcellular organelles including platelet-dense granules, melanosomes, and lysosomes. Our recent identification of the mutation in murine Rab geranylgeranyl transferase alpha-subunit gene (Rabggta) in one mouse model of HPS, the gunmetal mouse, suggested that human patients with similar phenotypes might have mutations in the human orthologous RABGGTA gene. This prompted reanalysis of the 5'-untranslated structure of the human RABGGTA gene in normal individuals and in patients with deficiencies of platelet-dense granules (alphadelta-SPD), alpha granules (alpha-SPD or gray platelet syndrome, GPS) or alpha plus dense granules (alphadelta-SPD). We report the complete sequence of intron alpha of RABGGTA and demonstrate that exon alpha is immediately upstream of intron alpha. The exon/intron structural organization of the 5'-untranslated region (UTR) of human RABGGTA was found to be similar to that of the mouse Rabggta gene. However, exons alpha and introns alpha are not homologous between mouse and human. Features of the 5'-UTR of RABGGTA suggest it is a housekeeping gene. While obvious disease-causing mutations of human RABGGTA were not found in our existing SPD patients by sequencing its entire coding region, several polymorphisms of RABGGTA including a putative cryptic splicing mutation in intron 4 were identified. Knowledge of the 5'-UTR structure of RABGGTA and its common polymorphisms will be useful for mutation screening or linkage analysis in patients with albinism, thrombocytopenia, or platelet SPD.

Expression of the thimet oligopeptidase gene is regulated by positively and negatively acting elements

Thimet oligopeptidase (TOP) is a thiol-dependent metallopeptidase, which can cleave and thereby modulate the activity of many neuropeptides. The enzyme is active in many endocrine tissues, including testis, brain, and pituitary. In rat, the richest source of TOP is the testes, with a specific activity fivefold that of brain. The mechanism whereby rat TOP expression is regulated at the transcriptional level has been examined by reporter gene assay and electromobility shift assays after isolation of 1020 bp of upstream sequence. Computer analysis predicts a number of potential transcription factor-binding sites, which were examined by deletion analysis and DNA-binding studies. The promoter or its deletion fragments were fused to luciferase reporter gene vectors and introduced into GH3 pituitary, COS-1 kidney, MAT-Lu prostate, and GC-2spd(ts) spermatid cells. Two regions of the promoter have been identified: a positively acting region (-901/-219) and a strong negatively acting region (-219/-102). Concomitantly, potential transcription factors interacting with the cis-acting elements of the promoter were studied by gel electromobility shift assays. This work has identified a number of transcription factor-binding sites. However, no differences in the binding behavior in the various cell lines was observed.

Auto-activation of the rta gene of human herpesvirus-8/Kaposi's sarcoma-associated herpesvirus

Rta, mainly encoded by open reading frame 50 (ORF50), is the product of an immediate-early gene of human herpesvirus-8 (HHV-8)/Kaposi's sarcoma-associated herpesvirus. Rta is a transcriptional activator that is both necessary and sufficient to disrupt viral latency and activate the expression of downstream viral lytic genes. We report that ectopically expressed Rta protein could also activate the rta promoter on a reporter plasmid up to 144-fold, both in latently infected B cells and in uninfected epithelial cells, and that this activation was dose-dependent. Furthermore, by analysing the 5' untranslated region using ribonuclease protection assays, we demonstrated that transfection of an Rta expression plasmid into latently infected cells activated the expression of rta transcripts from endogenous viral genomes. We propose that auto-activation of the immediate-early gene, rta, is an important strategy for HHV-8 to effectively respond to environmental stimuli and maximally activate the virus lytic cycle.

Genomic organization of the JEM-1 (BLZF1) gene on human chromosome 1q24: molecular cloning and analysis of its promoter region

The Jem-1 (JEM-1, HGMW-approved symbol BLZF1) gene mapping to human chromosome 1q24 codes for a ubiquitously expressed 3-kb mRNA, translated in a 45-kDa nuclear protein. Recent studies have shown a deficient expression of this gene in acute promyelocytic leukemia (APL). However, treatment with retinoids was able to upregulate JEM-1 mRNA in maturing NB4 leukemia cells. Here, we report the characterization of the structural organization of JEM-1. By hybridization screening of a human genomic library derived from blood mononuclear cells, five overlapping genomic DNA clones were isolated. These clones extend over 34 kb of the human genome and comprise the complete JEM-1 gene and a 4-kb 5'flanking region. Determination of the exon-intron structure of Jem-1 revealed seven exons whose junctions with introns exhibited typical splice sequences. A shorter transcript (Jem-1s, 1.3 kb) generated by exon 3 extension and polyadenylation was identified. Its translation generated a 23-kDa protein that exhibited a cytoplasmic localization. 5'RACE-PCR identified a major transcription start site (TSS) located at 403 nt upstream of the ATG. Computer analysis of the 1. 8-kb 5'flanking region showed that it lacks a TATA box, Inr motifs or DPE motifs, but it contains a typical CCAAT box located 95 bp upstream of the TSS. Sequencing also revealed potential cis-acting elements for multiple transcription regulators including Sp1, GATA, C/EBP, AP-1, and Pu1. No retinoic acid receptor elements or retinoic X receptor elements were detected. This 1.8-kb DNA sequence showed a strong constitutive promoter activity determined by a luciferase-reporter gene assay in transiently transfected HeLa cells. Retinoids further increased luciferase expression 2.7-fold. We demonstrated that the 1-kb distal sequence contains yet unidentified elements reducing constitutive transcription. Thus, the maximal constitutive promoter activity was assigned to a -432 + 101 region overlapping the TSS. These data support the idea of a constitutive expression of JEM-1, but a negative regulation in APL released by retinoids.

CART classification of human 5' UTR sequences

A nonredundant database of 2312 full-length human 5'-untranslated regions (UTRs) was carefully prepared using state-of-the-art experimental and computational technologies. A comprehensive computational analysis of this data was conducted for characterizing the 5' UTR features. Classification and regression tree (CART) analysis was used to classify the data into three distinct classes. Class I consists of mRNAs that are believed to be poorly translated with long 5' UTRs filled with potential inhibitory features. Class II consists of terminal oligopyrimidine tract (TOP) mRNAs that are regulated in a growth-dependent manner, and class III consists of mRNAs with favorable 5' UTR features that may help efficient translation. The most accurate tree we found has 92.5% classification accuracy as estimated by cross validation. The classification model included the presence of TOP, a secondary structure, 5' UTR length, and the presence of upstream AUGs (uAUGs) as the most relevant variables. The present classification and characterization of the 5' UTRs provide precious information for better understanding the translational regulation of human mRNAs. Furthermore, this database and classification can help people build better computational models for predicting the 5'-terminal exon and separating the 5' UTR from the coding region.

Sequence-motif analysis of 5'-untranslated region of GB virus-C in Japanese patients

BACKGROUND

GB Virus C (GBV-C) is considered to belong to the Flaviviridae; however, the structures of the N-terminal end of its putative polyprotein are not well known. The internal ribosomal entry site (IRES) at the 5'-untranslated region of GBV-C and an initiating codon at nucleotides (nt) 552-554 have been proposed. We investigated the validity of this proposal.

METHODS

The 5'-untranslated region of GBV-C was amplified from serum samples of 17 Japanese patients. Polymerase chain reaction-amplified products were directly sequenced and the obtained sequences were analysed by comparing them with the IRES structure of other viruses.

RESULTS

Fifteen of the 17 (88%) GBV-C strains in our patients were classified as being Asian type. The box-A-like sequence (UUUC) and box-B-like sequence (AUCAUGG) observed in the IRES of picornaviruses were highly conserved in all the strains. Based on pair-wise comparisons with the multiple alignment data, overall sequence divergence for the 5'-terminus was 2.9-12%. When compared with the proposed secondary structure of the IRES model, the sequence divergences of the Asian-type GBV-C were higher at the regions of loop structures and lower at the regions of double-stranded RNA. The AUG codons, except for the one located at nt 552-554, produced truncated polyproteins or were not in-frame with the putative protein.

CONCLUSIONS

Our examination of the sequence motif of GBV-C supports the proposal that the GBV-C has common structural motifs for IRES at its 5'-untranslated region and the AUG codon at nt 552-554 may be an initiating codon.

Tissue-specific expression of multiple mRNA variants of the mouse estrogen receptor alpha gene

The isolation of five new mouse estrogen receptor alpha mRNA variants (mERalpha A, B, F1, F2 and H) is described. All of these transcripts are generated by alternative splicing and all encode the 66 kDa ERalpha protein that the previously identified mRNA C variant generates. However, these transcripts differ in their 5' untranslated regions. RT-PCR and S1 nuclease protection assays revealed a tissue- and sex-specific expression pattern of all variants. The C and F mRNA variants are the predominantly expressed mERalpha variants in mouse. The expression of mERalpha H mRNA is restricted to liver, although female mice produce around a five fold higher level of this transcript than males. Our results show that the mERalpha gene is a complex genomic unit in mice that exhibits alternative splicing which is regulated in a tissue-specific manner.

Two linked mutations in transcriptional regulatory elements of the CYP3A5 gene constitute the major genetic determinant of polymorphic activity in humans

Cytochrome P450 3A subfamily members (CYP3A) are the most abundant liver cytochrome P450 forms, responsible for the biotransformation of over 50% of all drugs. The expression and activity of isoforms CYP3A4 and CYP3A5 show wide inter-individual variation, influencing both drug response and disease susceptibility. The molecular basis for this variation has never been defined. In this study, we used midazolam to characterize CYP3A5 phenotype in a panel of liver samples. A clear bimodality in metabolism was observed. Analysis of the 5' flanking region of the CYP3A5 gene identified two linked polymorphisms, T-369G and A-45G, located in transcriptional regulatory elements which are associated with increased expression and activity of the gene. A polymerase chain reaction based detection assay is described facilitating future studies into both the metabolic consequences of this variation and disease association studies relating to CYP3A5.

Distribution of hepatitis C virus genotypes in patients with chronic hepatitis C in northern Estonia

Distribution of hepatitis C virus (HCV) genotypes among 30 patients with chronic liver diseases and antibodies to HCV (anti-HCV) was investigated. Sera of these patients were analyzed for HCV genotype by reverse transcription-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP) analysis of the 5'-non-coding region (5'-NCR) of the virus genome and for HCV serotype by detecting antibodies to HCV NS4 peptides by enzyme-linked immunosorbent assay (ELISA). The following distribution of genotypes was found: genotypes 1b in 32.0%, 3a in 20.0%, 2a in 12.0% and 1a/b (double infection) in 28.0%. The results of serotyping were interpretable in 92.0% and concordant with those of genotyping in 80.0% of the patients. In Northern Estonia, the genotypes 1b and 3a seem to be most common in chronically infected patients. Serotyping is an generally available and cheap assay and can be performed in most diagnostic laboratories in comparison to genotyping. However, genotyping is a more sensitive and more specific assay.

Prominent expression of the selenoprotein thioredoxin reductase in the medullary rays of the rat kidney and thioredoxin reductase mRNA variants differing at the 5' untranslated region

The mammalian selenoprotein thioredoxin reductase is a central enzyme in protection against oxidative damage or the redox control of cell function. Previously a neuroblastoma-cell-derived 2193 bp cDNA for rat thioredoxin reductase 1 (TrxR1) was characterized [Zhong, Arnér, Ljung, Aslund and Holmgren (1998) J. Biol. Chem. 273, 8581-8591]. Here, the major rat TrxR1 mRNA was determined as 3.5 kb by Northern blotting. A corresponding full-length 3360 bp liver-derived cDNA was cloned and sequenced, being extended in the 3' untranslated region (3' UTR) compared with the previous clone. Among tissues examined, lowest TrxR1 mRNA levels were found in spleen and testis and highest in liver and kidney. High expression in kidney was unexpected and in situ hybridization of adult rat kidney was performed. This revealed a highly structured expression pattern with the mRNA being prominently synthesized in the proximal tubules of the medullary rays. Analysing rat kidney cDNA, a 5' UTR domain of TrxR1 was found that was different from that in liver- or neuroblastoma-derived cDNA clones. The kidney-derived 5' UTR mRNA domain was instead highly similar to kidney-derived cDNA variants of murine apolipoprotein E. By sequence determination of the rat genomic sequence upstream of the open reading frame for TrxR1, an exon was encountered that encoded a third alternative 5' UTR domain that could also be expressed, as confirmed by its presence in a mouse skin TrxR1 cDNA clone. It can therefore be concluded that TrxR1 mRNA is expressed in at least three different variants that differ at their 5' UTRs.

Expression of mitochondrial protein-coding genes in Tetrahymena pyriformis

In the ciliate protozoon, Tetrahymena pyriformis, mitochondrial protein-coding genes are highly divergent in sequence, and in a number of cases they lack AUG initiation codons. We asked whether RNA editing might be acting to generate protein sequences that are more conventional than those inferred from the corresponding gene sequences, and/or to create standard AUG initiation codons where these are absent. However, comparison of genomic and cDNA sequences (the latter generated by reverse transcriptase sequencing of T. pyriformis mitochondrial mRNAs) yielded no evidence of mitochondrial RNA editing in this organism. To delineate the 5' ends of mitochondrial protein-coding transcripts, primer extension experiments were conducted. In all cases, 5' termini were found to map within a few nucleotides of potential initiation codons, indicating that T. pyriformis mitochondrial mRNAs have little or no 5' untranslated leader sequence. The pattern of strong primer extension stops suggested that both standard (AUG) and non-standard (AUU, AUA, GUG, UUG) initiation codons are utilized by the Tetrahymena mitochondrial translation system. We also investigated expression of the nad1 gene, which in both T. pyriformis and Paramecium aurelia is split into two portions that are encoded by and transcribed from different DNA strands. Northern hybridization analysis showed that the corresponding transcripts are not trans-spliced, implying that separate N-terminal and C-terminal portions of Nad1 are made in this system. Finally, in a search for primary transcripts, we isolated from a T. pyriformis mitochondrial fraction several small RNAs that were reproducibly labeled by incubation in the presence of [alpha-(32)P]GTP and guanylyltransferase. Partial sequence information revealed that none of these cappable RNAs is encoded in the T. pyriformis mitochondrial genome.

Effect of increasing dose of interferon on the evolution of hepatitis C virus 1b quasispecies

The effects of interferon therapy on hepatitis C virus (HCV) genome are still controversial in terms of biological and clinical significance. Changes in the quasispecies of the hypervariable (HVR) and non-structural 5A (NS5A) regions of HCV 1b were evaluated in nine patients treated with increasing doses of interferon and five untreated controls. HCV quasispecies were analyzed in HVR and NS5A by single-strand conformation polymorphism assay. The HVR quasispecies varied over time both in treated and untreated patients. However, at least one persistent strain was present in all patients. With low doses of interferon, variations in HVR complexity were found in seven of nine patients and in four patients new variants became detectable. A reduction in the heterogeneity of the HVR quasispecies was observed after increase of the interferon dose. In contrast, NS5A profiles remained unmodified in all but three cases in which direct sequencing showed no changes in amino acid sequences of the predominant strain. The results suggest that interferon sensitivity of some HCV strains may be dose dependent. The homogeneity of NS5A pattern populations during treatment suggests that interferon exerts much less pressure on this region.

Selection of genetic variants of the 5' noncoding region of hepatitis C virus occurs only in patients responding to interferon alpha therapy

Interferon alpha (IFN alpha) can suppress the replication of hepatitis C virus (HCV) in chronically infected patients. However, HCV persists in a significant number of patients despite the normalization of alanine transaminase (ALT) during IFN alpha therapy. In this study, HCV variants in patients under IFN alpha therapy were characterized to examine their role in viral persistence during the therapy. Sixteen patients selected for this study were infected with HCV genotype 1b and remained HCV RNA positive for at least 1 month after onset of therapy. Nine patients responded to the therapy in terms of normalization of ALT (responders), whereas seven patients did not show a significant decrease of ALT level (nonresponders). To examine HCV populations in these patients, the HCV 5' noncoding region (5' NCR) was analyzed by polymerase chain reaction amplification and sequencing. Newly emerging variants of the HCV 5' NCR replaced predominant variants present prior to IFN alpha therapy in six of nine responders. Most predominant HCV variants during IFN alpha therapy carried a nucleotide substitution G to A at nt 231 within the 5' NCR. An analysis of the HCV quasispecies population in one responder revealed that a preexisting variant became predominant under IFN alpha therapy. These results emphasized the importance of the genetic heterogeneity of the HCV genome for viral resistance to IFN alpha. Five of seven HCV isolates from nonresponders were identical to those found in responders with regard to the nucleotide sequence of the 5' NCR. However, no selection of variants of the HCV 5' NCR occurred in nonresponders during the course of therapy. We conclude that IFN alpha treatment leads to the selection of variants of the HCV 5' NCR only in responders and may act differently in nonresponders. Our results suggest that the HCV 5' NCR may be a target of anti-HCV actions of IFN alpha.

Analysis of the 5' and 3'UTRs in the post-transcriptional regulation of the interleukin-5 gene

Post-transcriptional regulation is emerging as an important control point in cytokine gene expression. However, the role that it plays in IL-5 gene expression is unclear with some conflicting reports. Here we investigate the importance of post-transcriptional regulation and the role of the 5' and 3' untranslated regions (UTRs) in mIL-5 gene expression. To do this, IL-5 expression from a panel of cDNA constructs was compared. We found it essential to remove the 5' synthetic oligonucleotide tails, introduced during the cloning of the mIL-5 cDNA, when studying IL-5 expression. The presence of these oligo(G) tails acted as potent inhibitors of translation of both SV40 and SP6 transcripts. Furthermore, the length of the tails was found to be critical to the translational efficiency. Taking this into account, we found no evidence to suggest that IL-5 is regulated at the level of mRNA stability or translation efficiency by either the 5' or 3'UTR. These results suggest that post-transcriptional control is not a major factor regulating IL-5 expression.

Identification of a novel GB type C virus/hepatitis G virus subtype in patients with hematologic malignancies

The existence of four GB C virus/hepatitis G virus (GBV-C/HGV) subtypes has been reported. The subtype was determined in 16 multitransfused GBV-C/HGV infected patients prior to bone marrow transplantation by comparing the 5' untranslated region (5' UTR) sequence with 39 available sequences. Phylogenetic and bootstrap analyses were carried out with PHYLIP package 3.5c. In the samples with undefined subtype, the whole 5' UTR was cloned and sequenced. Comparison of distances showed that the isolates from 12/16 and 4/16 patients belonged theoretically to subtypes 2a and 2b, respectively. The phylogenetic tree and bootstrap analyses confirmed this result in only 11/16 samples. Analysis of the entire 5' UTR from the remaining five samples with undefined GBV-C/HGV subtype revealed genomic variability within the isolates from each patient and between the isolates of different patients. Evolutionary distances, phylogenetic tree, and bootstrap showed that the isolates from these samples were grouped in a separate branch, different from the published subtypes. In conclusion, a novel GBV-C/HGV subtype was found in a group of multitransfused patients with GBV-C/HGV infection.

Identification and characterization of a JC virus pentanucleotide repeat element binding protein: cellular nucleic acid binding protein

The JC virus (JCV) control region contains AGGGAAGGGA, the tandem pentanucleotide repeat element (Pnt2). Several proteins specifically interacted via Pnt2 to regulate the expression of JCV early promoter-enhancer (JCV(E)) or late promoter-enhancer (JCV(L)). In this study, a JCV Pnt2 oligonucleotide probe was used to screen a cDNA expression library from glial P19 mouse embryonal carcinoma cells. A cDNA clone was isolated by Southwestern blot assay and it produced a protein that reproducibly and specifically bound to Pnt2. This cDNA had 100% homology to one of three previously identified mouse cDNAs called cellular nucleic acid binding proteins (Cnbps). Cnbps are a highly homologous family of eukaryotic genes implicated in functional interactions with cytoplasmic RNA and regulatory DNA elements. An mRNA of 2.2 kb of Pnt2-interacting Cnbp (PCnbp) was seen in undifferentiated, muscle or glial P19 cells. When expressed from a cDNA expression vector as a fusion protein that also contained 115 kDa from beta-galactosidase, a Pnt2 binding protein (PCNBP) specifically bound to Pnt2 in Southwestern blots as a 30 kDa component of the 145 kDa fusion protein. Furthermore, JCV(E) expression was negatively regulated by PCnbp produced in vivo from the cDNA expression vector. Regulation of JCV(L) was unaffected. We suggest a novel role for CNBP as a PCNBP that interacts with Pnt2 in the negative transcriptional regulation of JCV(E).