Cloned DNA Sequences Research Articles

Cloning of DNA sequences localized on proximal fluorescent chromosome bands by microdissection in Pinus densiflora Sieb. & Zucc.

Japanese red pine, Pinus densiflora, has 2n=24 chromosomes, of which most carry chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI) bands at their centromere-proximal regions. It was proposed that these regions contain highly repetitive DNA. The DNA localized in the proximal fluorescent bands was isolated and characterized. In P. densiflora, centromeric and neighboring segments of the somatic chromosomes were dissected with a manual micromanipulator. The centromeric DNA was amplified from the DNA contained in dissected centromeric segments by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) and a cloned DNA library was constructed. Thirty-one clones carrying highly repetitive DNA were selected by colony hybridization using Cot-1 DNA from this species as a probe, and their chromosomal localization was determined by fluorescent in situ hybridization (FISH). Clone PDCD501 was localized to the proximal CMA band of 20 chromosomes. This clone contained tandem repeats, comprising a 27 bp repeat unit, which was sufficient to provide the proximal FISH signal, with a 52.3% GC content. The repetitive sequence was named PCSR (proximal CMA band-specific repeat). Clone PDCD159 was 1700 bp in length, with a 61.7% AT content, and produced FISH signals at the proximal DAPI band of the remaining four chromosomes. Four clones hybridized strongly to the secondary constriction and gave weak signals at the centromeric region of several chromosomes. Clone PDCD537, one of the four clones, was homologous to the 26S rRNA gene. A PCR experiment using microdissected centromeric regions suggested that the centromeric region contains 18S and 26S rDNA. Another 24 clones hybridized to whole chromosome arms, with varying intensities and might represent dispersed repetitive DNA.

Cloning of Random Oligonucleotides to Create Single-Insert Plasmid Libraries

Random double-stranded oligonucleotides are useful reagents to identify the optimal binding sites for DNA-binding proteins, such as transcriptional activators. Some applications require ligation of random oligonucleotides to form plasmid-based libraries such as the yeast one-hybrid system, where the activation of a cloned DNA sequence from a library of random DNA-binding sequences activates a reporter gene. Current theories do not account for the low efficiencies of oligonucleotide-based plasmid library construction methods. We developed a technique to clone single oligonucleotides into plasmid vectors with high efficiency that predictably results in only one oligonucleotide insert per colony and used this method to clone a yeast one-hybrid library. This method, either as presented or with modifications, should be suitable for any situation where high-efficiency cloning of single oligonucleotide inserts is desired.

Hybridization to oligonucleotide arrays for the assessment of gene copy number

Array-based comparative genomic hybridization (CGH) provides a higher-resolution and more quantitative alternative to chromosome CGH for the assessment of abnormalities in genomic copy number. In array-based CGH analyses published to date, array elements have been composed of cloned DNA sequences (such as P1s, BACs or complementary DNAs), and thus copy number abnormalities can be mapped from data on the genomic mapping of such clones. These advanced methods are limited by difficulties in the production of cloned DNAs and distortions in the data arising from elements in the arrays that are present at multiple copies in the normal genome. To overcome some of these limitations, we have produced a low-complexity probe based on the polymerase chain reaction (PCR). In oligonucleotide array CGH, probes are prepared by multiplex PCR amplification using 10−50 primer pairs. Two 50-base oligonucleotides that map between the primer pairs serve as array elements. Because the linearity of this method apparently depends on primer complexity during PCR, we substituted adapter sequences (which make up the 5' end of our PCR primers). We compared the performances of T7 and R24 adapters in a 24-plex PCR with one another and with previously obtained copy number data on several chromosome 20 loci in MCF7 cells obtained from fluorescence in situ hybridization. We found that use of the T7 adapters improved the amplitude of test-to-reference ratios 2.3-fold, suggesting less-dampened ratios and increased linearity in our assessment of copy number by this method. We will demonstrate the large-scale application of oligonucleotide array CGH to ovarian and breast cancer samples.

Two Isoforms of Trimming Glucosidase II Exist in Mammalian Tissues and Cell Lines but Not in Yeast and Insect Cells

We previously cloned glucosidase II and provided in vivo evidence for its involvement in protein folding quality control. DNA-sequencing of different clones demonstrated the existence of two isoforms of glucosidase II which differed by 66 nucleotides due to alternative splicing. The existence of two enzyme isoforms in various organs of pig and rat as well as human, bovine, rat, and mouse cell lines could be demonstrated by RT-PCR and Western blotting. Furthermore, the two isoforms of glucosidase II could be detected in embryonic and postnatal rat kidney and liver. In yeast, Saccharomyces cerevisiae, and in insects, Drosophila S2 cells, only one isoforms of the enzyme was detectable. The ubiquitous occurrence of the two glucosidase II isoforms in mammalian tissues and cell lines might be indicative of a special function of each isoform.

Cloning and characterization of NBS-LRR class resistance-gene candidate sequences in citrus

Numerous disease resistance gene-like DNA sequences were cloned from an intergeneric hybrid of Poncirus and Citrus, using a PCR approach with degenerate primers designed from conserved NBS (nucleotide-binding site) motifs found in a number of plant resistance genes. Most of the cloned genomic sequences could be translated into polypeptides without stop codons, and the sequences contained the characteristic motifs found in the NBS-LRR class of plant disease resistance genes. Pairwise comparisons of these polypeptide sequences indicated that they shared various degrees of amino-acid identity and could be grouped into ten classes (RGC1–RGC10). When the sequences of each class were compared with known resistance-gene sequences, the percentage of amino-acid identity ranged from 18.6% to 48%. To facilitate genetic mapping of these sequences and to assess their potential linkage relationship with disease resistance genes in Poncirus, we developed CAPS markers by designing specific primers based on the cloned DNA sequences and subsequently identifying restriction enzymes that revealed genetic polymorphisms. Three of the amplified DNA fragment markers (designated as 18P33a, Pt9a, and Pt8a) were associated with the citrus tristeza virus resistance gene (Ctv), and one fragment (Pt8a) was associated with the major gene responsible for the citrus nematode resistance (Tyr1); both genes are from Poncirus and of importance to citrus survival and production. These polymorphic fragments were located on two local genetic linkage maps of the chromosome region from Ctv to Tyr1. These results indicate that resistance-gene candidate sequences amplified with the NBS-derived degenerate primers are valuable sources for developing markers in disease resistance-gene tagging, mapping, and cloning.

Molecular cloning and phylogenetic analysis of a cDNA encoding the cat ( Felis domesticus) Ig epsilon constant region

A feline splenic cDNA library was screened with a 32P-labelled cDNA probe encoding the canine IgE epsilon heavy chain subunit. A cDNA sequence of 1614 nucleotides encoding the complete feline IgE heavy chain, as well as a portion of a variable region, was identified. A search of the GenBank database revealed an identity of 82% at the nucleotide level and 76% at the amino acid level between the feline epsilon heavy chain sequence and the canine homologue. In a separate study, feline genomic DNA, isolated from whole feline embryo cells, was subjected to PCR amplification using primers based on known partial genomic DNA sequences for the feline Cε gene. Following removal of an intron from the 683 bp PCR product, the coding sequence yielded an ORF of 506 bp. The DNA sequence of this PCR clone differed by a single nucleotide from the cDNA clone. This difference is silent, and therefore the proteins encoded by the two sequences are identical over the regions cloned and sequenced. Phylogenetic analysis of the constant regions of nine immunoglobulin epsilon genes revealed that the feline cDNA is most similar to the canine homologue.

In vitro selection of mutations in the human immunodeficiency virus type 1 reverse transcriptase that decrease susceptibility to (-)-beta-D-dioxolane-guanosine and suppress resistance to 3'-azido-3'-deoxythymidine.

Human immunodeficiency virus type 1 (HIV-1) isolates resistant to (-)-beta-D-dioxolane-guanosine (DXG), a potent and selective nucleoside analog HIV-1 reverse transcriptase (RT) inhibitor, were selected by serial passage of HIV-1(LAI) in increasing drug concentrations (maximum concentration, 30 microM). Two independent selection experiments were performed. Viral isolates for which the DXG median effective concentrations (EC(50)s) increased 7.3- and 12.2-fold were isolated after 13 and 14 passages, respectively. Cloning and DNA sequencing of the RT region from the first resistant isolate identified a K65R mutation (AAA to AGA) in 10 of 10 clones. The role of this mutation in DXG resistance was confirmed by site-specific mutagenesis of HIV-1(LAI). The K65R mutation also conferred greater than threefold cross-resistance to 2',3'-dideoxycytidine, 2', 3'-dideoxyinosine, 2',3'-dideoxy-3'-thiacytidine, 9-(2-phosphonylmethoxyethyl)adenine, 2-amino-6-chloropurine dioxolane, dioxolanyl-5-fluorocytosine, and diaminopurine dioxolane but had only marginal effects on 3'-azido-3'-deoxthymidine (AZT) susceptibility. However, when introduced into a genetic background for AZT resistance (D67N, K70R, T215Y, T219Q), the K65R mutation reversed the AZT resistance. DNA sequencing of RT clones derived from the second resistant isolate identified the L74V mutation, previously reported to cause ddI resistance. The L74V mutation also decreased the AZT resistance when the mutation was introduced into a genetic background for AZT resistance (D67N, K70R, T215Y, T219Q) but to a lesser degree than the K65R mutation did. These findings indicate that DXG and certain 2',3'-dideoxy compounds (e.g., ddI) can select for the same resistance mutations and thus may not be optimal for use in combination. However, the combination of AZT with DXG or its orally bioavailable prodrug (-)-beta-D-2, 6-diaminopurine-dioxolane should be explored because of the suppressive effects of the K65R and L74V mutations on AZT resistance.

Genetic characterization of HIV type 1 and type 2 from Bissau, Guinea-Bissau (West Africa)

Previous studies from Guinea-Bissau (West Africa) have demonstrated a unique epidemiology with respect to both HIV-1 and HIV-2 infection. In order to evaluate the prevalence and dynamics of HIV-1 and HIV-2 subtypes in Bissau, the capital city of Guinea-Bissau, a cross-sectional study was set up using serological and molecular techniques. Plasma samples from 103 individuals were screened for HIV-1 and HIV-2 antibodies by ELISA and Western-blot. Seropositive results were confirmed by PCR amplification of proviral sequences in primary peripheral blood mononuclear cells (PBMC) with env and LTR primer sets for HIV-2 and env, LTR and pol primers for HIV-1. A total of 38/103 individuals were HIV-seroreactive (four HIV-1, 15 HIV-2, 19 HIV-1/HIV-2). A total of eight out of 19 dually seropositive specimens showed double PCR amplification of HIV-1 and HIV-2 proviral sequences, accounting for 21% of the infected individuals. In the remaining 11 individuals either HIV-2 or HIV-1 sequences were detected, the majority ( n=9) amplifying only HIV-2. These screening data demonstrate a high discrepancy between serology and PCR results for dually seroreactive samples, Western-blot giving an overestimation of double infection. Additionally, HIV-1 strains were subtyped by heteroduplex mobility assay (HMA) on the basis of gp120 sequences. Subtyping of HIV-2 was carried out by DNA sequencing and phylogenetic analysis of env V3 molecular clones. For both HIV-1 and HIV-2 strains circulating in Bissau, our results indicate dominance of subtype A.

The BLAST algorithms: practical application in molecular cloning, marker-assisted selection (MAS) and introgression of wheat.

BLAST (Basic Local Alignment Search) analyses of Hordeum chilense RAPD markers have shown DNA sequence similarities with several plant genes. Biologically significant hits were scored for: plastocianin (Hordeum vulgare), alpha-gliadin (Triticum aestivum), Grandel-6 retrotransposon (Zea diploperennis), retrofit (gag/pol) copia-like, transposon-like element (Oryza longistaminata), copia-like retrotransposon Hopscotch polyprotein (gag/pol) (Zea mays) and several retrotransposons/retroelements from other species (Arabidopsis thaliana, Oryza sativa, Pisum sativum and Zea mays). Statistically significant hits also included endochitinase (Brassica napius), ribulose-1,5-bisphosphate carboxylase (Euglena gracilis), piruvate, orthophosphate dikinase (Flaveria trinervia), and an ORF flanked by ARS sequences (Triticum aestivum). Interestingly, it was also found that the currently recommended BLAST algorithm (version 2.0.11; gapped) at <http://www.ncbi.nlm.nih.gov> did not produce any biologically significant hits, whereas the previous version (1.4.11; ungapped) did generate biologically significant results. Thus, we suggest using the new BLAST 2.0.x when strong homologies are expected in short sequence stretches between closely related species. In other instances (and particularly when searching for lower similarities, yet spanning significantly larger stretches between more distant species), the BLAST 1.4.x could yield additional results. BLAST searches are valuable tools to identify and clone DNA sequences of interest, with applications in Marker-Assisted Selection (MAS) and wheat introgression.

Deduced Amino Acid Sequence of an α‐Gliadin Gene from Spelt Wheat (Spelta) Includes Sequences Active in Celiac Disease

ABSTRACTThe complete amino acid sequence of an α‐type gliadin from spelt wheat (spelta) has been deduced from the cloned DNA sequence and compared with α‐type gliadin sequences from bread wheat. The comparison showed only minor differences in amino acid sequences between the α‐type gliadin from bread wheat and the α‐type gliadin from spelta. The two sequences had an identity of 98.5%. Larger differences can be found between different α‐type gliadin amino acid sequences from common bread wheat. Because all the different classes of gliadins, α, β, γ, and ω, appear to be active in celiac disease, it is reasonably certain that the spelta gliadin is also toxic. We conclude that spelta is not a safe grain for people with celiac disease, contrary to the implications in labeling a bread made from spelta as “an alternative to wheat”. Our conclusions are in accord with spelta and bread wheat being classed taxonomically as subspecies of the same genus and species, Triticum aestivum L.

CDNA cloning and expression of Carica papaya prochymopapain isoforms in Escherichia coli

Chymopapain is one of the four known cysteine proteinases found in the latex of Carica papaya. DNA sequencing of clones derived from a leaf cDNA library identified five cDNA types coding for precursor chymopapains. All of these isoforms have a free cysteine residue at position 117, characteristic of chymopapain. Two of the isoforms possess a further free cysteine residue, which is not likely to be involved in disulphide bonds or the active site apparatus. Another amino acid substitution found in two of the isoforms at position 133 is predicted to lie in the S2 subsite of the substrate binding cleft. One of the prochymopapain isoforms was expressed in Escherichia coli. Protein was expressed as insoluble inclusion body material. This protein was solubilised, refolded and autocatalytically cleaved to yield mature chymopapain that had comparable kinetic constants to authentic native enzyme.

Functional analysis of DNA sequences located within a cluster of DNase U hypersensitive sites colocalizing with a MAR element at the upstream border of the chicken α‐globin gene domain

We have cloned and sequenced a genomic DNA fragment of chicken containing a cluster of DNase I hypersensitive sites (DHS) located 11-15 kb upstream from the first gene of the alpha-globin gene domain and including a constitutive DHS flanked by two erythroid-specific ones. A 1.2-kb subfragment of the DNA fragment under study located upstream to the constitutive DHS and colocalizing roughly with one of the erythroid-specific DHS was shown to possess the properties of a matrix association region (MAR). The cloned DNA sequences were tested for their ability to serve as promoters and/or influence transcription from the promoter of the alphaD globin gene. In the region studied, we did not find any promoters or enhancers that were active in erythroid cells. The whole DNase I hypersensitive region and some of its subfragments showed a silencing effect when placed downstream from the reporter gene. The expression of the reporter gene was completely abolished, however, when these DNA fragments were placed between the alphaD promoter and the reporter gene. Thus, they seem to act as transcription "terminators." Numerous polyadenylation signals (AATAAA) and an AT-rich palindrome were found within the sequenced DNA fragment. These observations are discussed within the frame of the hypothesis postulating that continuous transcription is essential for maintaining the active status of genomic domains. Furthermore, it is suggested that the DNA fragment studied contains a negative control element that keeps globin genes silent within the chromatin domain permanently open in nonerythroid cells.

Epitope Discovery Using Bacteriophage Display: The Minimum Epitope of an Anti-IRBP Antibody

The purpose of this study was to determine, using random peptide library (RPL) technologies, the minimal epitope requirements of the mouse monoclonal anti-interphotoreceptor-retinoid-binding protein antibody, H3B5. This previously characterized antibody is used as an example to examine whether RPL's offer a relatively easy and rapid route to obtaining detailed epitope mapping data.A pentadecamer random peptide library (RPL) displayed on the major coat protein (gene 8) of filamentous bacteriophage (F88-4-15) was used as a target for selection by the anti-IRBP monoclonal antibody, H3B5. Three rounds of library selection were performed, and 90 of the resultant RPL clones were examined for affinity to H3B5 by enzyme-linked immunosorbent assay (ELISA). DNA sequencing of ELISA positive clones provided sequence of the region encoding the random peptide.After three rounds of selection of the RPL, 76.7% of clones examined interacted with H3B5, 17.7% did not show significant binding and 6.6% bound to control antibody also. The essential elements of the peptide epitope were determined by sequence comparison of 24 clones to be the four amino-acid sequence (Aspartic or glutamic acid)-Proline-Arginine-(Leucine, Isoleucine or Valine). This motif [(D/E) PR (L/I/V)] is in agreement, but at greater resolution, than previous synthetic peptide studies where the motif AASEDPRL was identified. Other motifs were found which bound to H3B5 but did not share primary structure similarities (peptidomimetics).Selection from a RPL has rapidly defined the minimal requirements for the H3B5 epitope in fine detail. Such a process offers great potential for investigating antibody–antigen interactions and core sequences of an epitope, and enables the identification of motifs in other proteins which may be recognized by the antibody, providing information on possible cross-reactivity.

7] Cosmid-based exon trapping

Publisher Summary Exon trapping is a widely used gene identification method. In contrast to RNA-based methods, such as screening of cDNA libraries and cDNA selection, exon trapping is independent of gene expression. Exon trapping provides a functional assay in which cloned DNA sequences are selectively isolated based on the presence of functional splice sites. Consequently, sequences are isolated directly from the clone under analysis without knowledge or availability of tissues expressing the unknown gene. This chapter discusses cosmid based exon trapping that was developed to bypass problems related to plasmid-based exon trapping. It discusses the principle of cosmid-based exon trapping. The chapter also discusses reverse transcription (RT) and amplification by polymerase chain reaction (PCR), which is the most critical step of the entire procedure.

A 63 kDa Skeletal Muscle Protein Associated with Eye Muscle Inflammation in Graves' Disease is Identified as the Calcium Binding Protein Calsequestrin

It is generally accepted that thyroid-associated ophthalmopathy (TAO) is an autoimmune disease of the eye muscle (EM) and the surrounding orbital connective tissue in which circulating antibodies play an important role. Antibodies against EM membrane proteins of 63–67 kDa mol. wt. seem to be the best markers of ophthalmopathy in patients with autoimmune thyroid disease. We purified a 63 kDa EM protein using SDS-polyacrylamide gel electrophoresis technology and TAO patients' sera as probes, digested the protein with cyanogen bromide and sequenced immunoreactive peptides. We also screened a human EM library with a rabbit antiserum against 63–65 kDa proteins and affinity purified antibodies from a TAO patient's serum that reacted with a 55 kDa EM membrane protein. From partial sequence information and from DNA sequencing of positive cDNA clones, the protein was identified as calsequestrin, a 63 kDa calcium binding protein localized in the sarcoplasmic reticulum of the muscle fiber. As determined by Northern blotting, calsequestrin was expressed in EM and other skeletal muscle but not thyroid or fibroblasts. Calsequestrin is different from the “64 kDa protein”, which has been identified as succinate dehydrogenase flavoprotein subunit, which has a corrected mol. wt. of 67 kDa. Serum antibodies against calsequestrin were found in 40% of patients with clinically active TAO, but in only 4% of those with stable eye disease, and in 5% of normal subjects, by immunoblotting. Although it is possible that autoimmunity against calsequestrin plays a role in the progressive EM damage that characterizes ophthalmopathy it is more likely that the antibodies are secondary to a reaction against some other cell membrane protein, such as the novel thyroid and eye muscle shared protein G2s or the TSH receptor.

Application of AFLP Technique That Uses Non-radioactive Fluorescent Primers to the Detection of Genetic Diversity in Japanese Rice Cultivars and Cloning of DNA Sequences Derived from an Indica Genome.

To perform rapid amplified fragment length polymorphism (AFLP) analysis and efficiently clone AFLP fragments with non-radioactive primers, we modified the current AFLP protocol. When the modified procedure was applied to the rice genome, 30 to 80 AFLP fragments (∼40 to 400 bp in length) could be detected in a single PCR reaction. To assess the suitability of the technique for the analysis of the rice genome, we first applied it to quantify genetic diversity in a sample of 55 predominantly Japanese modern and domestic cultivars. In this analysis, more than 75% of the Japanese rices were differentiated by the combination of six prinrer pairs. Then we used the technique to identify and clone AFLP fragments unique to the Japanese variety Kinuhikari compared to those found in the closely related cultivar Koshihikari. In this cloning, we obtained sequences derived from chromosomal segments of an Indica genome, which had introgressed into the Kinuhikari genome. These two studies demonstrated that the modified AFLP technique is suitable for the genome analysis in rice.

Chromosomal homologies between Drosophila melanogaster and D. funebris determined by in-situ hybridization.

Seventeen biotin-labeled DNA sequences were hybridized to polytene chromosomes of Drosophila melanogaster and D. funebris in order to establish chromosomal homologies between these species. Ten probes correspond to cloned DNA sequences from D. melanogaster (RpII 215, MHC, H3-H4, Tor, hsp 68, hsp 28/23, hsp 83, PP1alpha, RpII 140, and ey), four are clones isolated from a D. subobscura genomic library (Xdh, lambdaDsubS3, lambdaDsubG3, and lambdaDsubG4), two are clones from D. funebris (F2 and Adh) and one from D. virilis (ci). The probes were chosen in order to cover all the autosomes, since X-chromosome homologies have already been studied by linkage analysis of morphological mutants. Most probes gave a unique hybridization signal; consequently, our results allow unambiguous inferences about chromosomal homologies. The results show extensive gene rearrangement within all chromosomal elements, probably due to paracentric inversions, but are consistent with Muller's proposal that chromosomal elements have conserved their genetic content during the evolution of Drosophila.

A Peptidomimetic Antagonist of TNF-α-Mediated Cytotoxicity Identified from a Phage-Displayed Random Peptide Library

Abstract Phage-displayed peptide libraries represent a vast collection of peptide sequences that can be used to identify novel therapeutic molecules. In this report, a 15-mer phage-displayed peptide library was used to identify potential TNF-α antagonists. After direct interaction of recombinant human TNF-α with the library, four randomly selected phage clones were shown to inhibit in a dose-dependent fashion both mouse and human TNF-α-induced cytotoxicity in vitro. DNA sequencing of the positive clones revealed a common amino acid sequence that does not bear any structural similarity to the known primary structures of the extracellular domains of either 55-kDa or 75-kDa TNF receptors. This sequence was synthesized, and the peptidomimotope was shown i) to bind to the recombinant human TNF-α using surface plasmon resonance (biosensor) technology and ii) to inhibit both recombinant mouse and human TNF-α-induced cytotoxicity in vitro in a dose-dependent fashion. These findings highlight the potential of phage-displayed random peptide libraries for the identification of novel low molecular antagonistic molecules that can block the biologic activities of TNF-α.

Cloning of two novel growth hormone transcripts expressed in human placenta.

Several isoforms of human GH (hGH) are produced by two related genes expressed in the pituitary (hGH-N) and in the placenta (hGH-V). These genes consist of five exons (denoted 1-5) separated by four introns (denoted A-D). In the present report, two new transcripts of the hGH-V gene are described. The coding region of the hGH-V gene was amplified by RT-PCR using placental complementary DNA as template. DNA sequencing of several clones revealed two novel transcripts. One had a 45-bp deletion caused by the use of an alternative splice acceptor site within exon 3, similar to that in the hGH-N gene, predicting a 20-kDa isoform of hGH-V. The other transcript was generated by the use of an alternative splice donor site causing a 4-bp deletion in the end of exon 4, predicting a 24-kDa protein with 219 amino acids, which we refer to as hGH-V3. The carboxy-terminal sequence of hGH-V3 differs from 22-kDa hGH-V and hGH-V2, the two previously reported transcripts of the hGH-V gene, and does not contain a predicted transmembrane domain as described for hGH-V2. Ligase chain reaction was then used to analyze the possible use of the same splicing pattern in transcripts derived from the other genes of the hGH-gene cluster. Alternatively spliced transcripts encoding the 20-kDa hGH isoform were detected from the hGH-N and hGH-V genes, but not from the human chorionic somatomammotropin-A/B genes. The alternative splicing generating hGH-V3 was only demonstrated in transcripts derived from the hGH-V gene. Using competitive RT-PCR, the expression of hGH-V3 was estimated to be 10% of the hGH-V messenger RNA in full-term normal placentas and in placentas from pathological pregnancies. The 20-kDa hGH-V was detected in two of four full-term normal placentas, whereas a weak signal was observed in one of the pathological placentas. We conclude that the hGH-V primary transcript undergoes alternative splicing pathways generating at least four different messenger RNAs, predicting the expression of different hGH isoforms, including two with a complete sequence divergence in the carboxy-terminus.

The genomic structure of the chicken ICSBP gene and its transcriptional regulation by chicken interferon.

The chicken interferon consensus sequence binding protein (ChICSBP) gene spans over 9 kb of DNA and consists, as its murine homolog, of nine exons. The first untranslated exon was identified by 5'-RACE technology. The second exon contains the translation initiation codon. Canonical consensus splice sites are found on every exon/intron junction. The introns are generally smaller than their mammalian counterparts. The ChICSBP and ChIRF-1 genes have been mapped by fluorescence in situ hybridization to different microchromosomes. The transcription start site has been mapped by primer extension. Inspection of the DNA sequence of a genomic clone containing the first exon and the region 1700-bp upstream revealed several potential cisregulatory elements of transcription. The ChICSBP mRNA is induced by recombinant ChIFN type I and ChIFN-gamma. A palindromic IFN regulatory element (pIRE) with high sequence homology to gamma activation site (GAS) sequences was functionally required in transient transfection assays for the induction of transcription by ChIFN-gamma.