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PubMed2002

The MDR1 polymorphisms at exons 21 and 26 predict steroid weaning in pediatric heart transplant patients.

Various polymorphisms of the MDR1 gene that encodes for P-glycoprotein (P-gp), a transmembrane pump, have been identified. A silent mutation C3435T in exon 26 and a G2677T mutation in exon 21 have been correlated with P-gp expression and function in humans. The objectives of this study were (a) to determine whether the MDR1 exon 21 and exon 26 polymorphisms were related to steroid weaning in a pediatric heart transplant (HTx) population, and (b) to determine whether an association exist between the MDR1 exon 21 and exon 26 polymorphisms in these patients. Sixty-nine pediatric HTx patients were studied. MDR1 genotyping was determined by polymerase chain reaction amplification, sequencing the DNA, and sequence evaluation using Polyphred software (University of Washington) to identify genotypes. The steroid dose at 1 year post-transplantation was recorded. For steroid weaning at one year post-HTx for MDR1 C3435T, 12 of 18 (67%) patients in the CC genotype were still on prednisone, whereas only 18 of 47 (38%) of the CT/TT group were still receiving prednisone (p = 0.04). Similar results were observed for the MDR1 G2677T genotyping and steroid weaning. Forty-three of 46 patients (93.5%) who have MDR1 C3435T allele also have a mutant G2677T allele (p < 0.001). We conclude that (a) a significantly larger number of MDR1 3435 CC HTx patients remain on steroids at 1 year after transplantation, and (b) the MDR1 C3435T genotype is associated with the G2677 genotype in pediatric HTx patients.

Adolescent↗

PubMed1997

A novel splice site mutation in the androgen receptor gene results in exon skipping and a non-functional truncated protein.

Mutations of the androgen receptor (AR) gene and protein are associated with complete androgen insensitivity syndromes (CAIS) in individuals with XY genotypes causing them to develop as phenotypic females. Splice site mutations of the AR gene are very rare and in this report we describe the consequences of a novel G --> A mutation at the exon 7/intron 7 splice junction of the AR gene that resulted in CAIS in two siblings. Reverse transcriptase-polymerase chain reaction (RT-PCR) of the AR transcript in patient's fibroblasts was performed and sequencing of the product showed omission of exon 7, with exon 6 being spliced directly to exon 8. This resulted in a shift of the reading frame and the introduction of a premature stop codon 10 amino acids into exon 8. Immunoblot analyses showed that the resultant AR protein was partially deleted in its C-terminal region and was approximately 1.5 kDa smaller than the wild type. This truncated AR was non-functional as it was unable to bind its physiological ligand (dihydrotestosterone) in androgen-binding assays. This is the first documentation of a point mutation in the AR gene which causes exon skipping and proves that the mutation is the cause of CAIS in our two subjects.

Androgens↗

PubMed1999

Presence of exon I.4 mRNA from CYP19 gene in human granulosa cells.

Estrogens are synthesized from C19 steroids by a unique form of cytochrome P450 aromatase. Expression of the human CYP19 gene involves tissue specific use of alternative promoters. In the present study, an RT-PCR procedure was used to amplify and quantify various transcripts expressed in human granulosa cells. Cells were aspirated together with follicular fluid from Periovulatory ovarian follicles present in ovaries of 14 patients undergoing a treatment for in vitro fertilization. Sequencing of PCR products demonstrated the presence of exon I.4-specific transcripts in addition to exon P.II, exon I.3 and I.3-truncate transcripts. Quantitative results confirmed that exon P.II specific transcripts were largely predominant compared to other exon-specific transcripts, and that exon I.4-specific transcripts were the least abundant.

Alternative Splicing↗

PubMed2000

Methylation of exon 2 of p16 is associated with late stage oesophageal cancer.

Methylation of the p16 gene was studied in 16 oesophageal tumours. Five (31%) of the tumours were found to be methylated in exon 1 and eight (50%) were methylated in exon 2. The loss of p16 protein correlated with methylation of exon 1 (P = 0.005). However, methylation of exon 2, but not exon 1, was found to be associated with late stage tumours (P = 0.01). We conclude that the methylation of exon 2 of p16 may have effects on the progression of oesophageal tumours that are independent of the expression of the p16 protein.

Adenocarcinoma↗

PubMed2002

Loss of mu-opioid receptor-mediated G-protein activation in the pons/medulla of mice lacking the exons 2 and 3 of mu-opioid receptor gene.

The G-protein activation induced by mu-opioid receptor agonists in the pons/medulla membrane obtained from mice lacking exons 2 and 3 of mu-opioid receptor gene (MOR (Exons 2 and 3)-knockout (KO) mice) was investigated by monitoring guanosine-5'-o-(3-[(35)S]thio)triphosphate ([(35)S]GTPgammaS) binding. The MOR agonists D-Ala2,MePhe4,Gly(ol)5)enkephalin, endomorphin-1 and endomorphin-2 each produced concentration-dependent increases in [(35)S]GTPgammaS binding to pons/medulla membrane in wild-type mice, but not in MOR (Exons 2 and 3)-KO mice. beta-Endorphin also produced a concentration-dependent increase of [(35)S]GTPgammaS binding to pons/medulla membrane in wild-type mice, however the increase of [(35)S]GTPgammaS binding induced by beta-endorphin was partially attenuated in MOR (Exons 2 and 3)-KO mice. The present results suggest that MOR that is created from the sequences encoded with exons 2 and 3 of the MOR gene, as has been previously observed in studies of mice lacking exon 1 of this gene, may be another critical target for the activation of G-protein by MOR agonists in the mouse pons/medulla.

Analgesics, Opioid↗

PubMed1999

Multiple 5'-untranslated exons in the nuclear respiratory factor 1 gene span 47 kb and contribute to transcript heterogeneity and translational efficiency.

Nuclear respiratory factor 1 (NRF-1) is a nuclear transcription factor that has been implicated in the nuclear control of respiratory chain expression in mammalian cells. Here, we demonstrate that a complex pattern of alternative splicing contributes to sequence heterogeneity within the human NRF-1 5'-untranslated region (UTR). At least six different 5'-UTR exons (UTRs 1-6) were detected in NRF-1 transcripts. These exons were mapped to human NRF-1 genomic clones and their sequences, including donor and acceptor splice junctions, determined. Two of the human UTR exons were derived from insertions of Alu-sq family members into the NRF-1 locus. The distance between the transcription initiation sites in UTR1 and the first protein coding exon is approx. 47kb, bringing the total length of the human NRF-1 gene to approx. 104kb. In contrast to human, only two UTR exons were found in mouse. The mouse UTR1 sequence obtained is identical to human UTR1, but mouse UTR2 bears no resemblance to any of the human exons. Mutations within human UTR1 modulate NRF-1 expression by interfering with mRNA translational efficiency in transfected cells and in an in vitro translation system. The effects of the mutations are proportional to their ability to disrupt predicted mRNA secondary structures within UTR1. Thus, the unusually high sequence conservation within UTR1 in part reflects selective constraints on translational expression.

5' Untranslated Regions↗

PubMed2000

Complete skipping of exon 66 due to novel mutations of the dystrophin gene was identified in two Japanese families of Duchenne muscular dystrophy with severe mental retardation.

Severe mental retardation is a rare complication of Duchenne muscular dystrophy (DMD). Here we report that two DMD cases showing severe mental retardation exhibit the same exon skipping event induced by different intron mutations. In the two Japanese DMD patients studied, the complete sequence of exon 66 of the dystrophin gene was found to be absent from the dystrophin mRNA, creating a premature stop codon in exon 67. Novel point mutations at the consensus sequence of the splice donor site of intron 66 (T9857(+2) to C in one case and G9857(+5) to T in the other case) were found to be the cause of complete exon skipping. Remarkably, severe mental retardation cosegregated with an exon 66-skipping event in their families. Furthermore, pachygyria was disclosed by magnetic resonance imaging (MRI) examination of the brain of one case. Our results suggested that exon 66 skipping should be examined in DMD cases with a severe form of mental retardation.

Adult↗

PubMed2002

Targeted exon skipping as a potential gene correction therapy for Duchenne muscular dystrophy.

Duchenne muscular dystrophy is primarily caused by frame-disrupting mutations in the Duchenne muscular dystrophy gene which abort dystrophin synthesis. We have explored a gene correction therapy aimed at restoration of the reading frame in Duchenne muscular dystrophy patients. Through the binding of antisense oligoribonucleotides to exon-internal sequences in the pre-mRNA, the splicing can be manipulated in such a manner that the targeted exon is skipped and a slightly shorter, but in-frame, transcript is generated. We recently showed that antisense oligoribonucleotide-mediated skipping of exon 46 efficiently induced dystrophin synthesis in cultured muscle cells from Duchenne muscular dystrophy patients carrying an exon 45 deletion. In this study we have identified antisense oligoribonucleotides with which the skipping of 11 other Duchenne muscular dystrophy exons could be induced in cultured human muscle cells. The targeted skipping of only one particular exon may restore the reading frame in a series of patients with different mutations. Accordingly, these antisense oligoribonucleotides would allow correction of over 50% of deletions and 22% of duplications reported in the Leiden DMD-mutation Database.

Base Sequence↗

PubMed1999

The ribosomal protein L34 gene from the mosquito, Aedes albopictus: exon-intron organization, copy number, and potential regulatory elements.

We describe the structural analysis of genomic DNA encoding ribosomal protein (rp) L34 from the mosquito, Aedes albopictus. Comparison of genomic DNA sequences encompassing approximately 8 kb with the rpL34 cDNA sequence showed that the gene contains three exons and two introns, encoding a primary transcript with a deduced size of 6196 nucleotides from the transcription start site to the polyadenylation site. Exon 1, which is not translated, measures only 45 bp, and is separated from Exon 2 by a 359 bp intron. Exon 2 measures 78 bp, and contains the AUG translation initiation codon 14 nucleotides downstream of its 5'-end. Downstream of Exon 2 is a 5270 bp intron, followed by the remainder of the coding sequence in Exon 3, which measures 444 bp including the polyadenylation signal. We used a novel PCR-based procedure to obtain 1.7 kb of DNA upstream of the rpL34 gene. Like the previously described Ae. albopictus rpL8 gene and various mammalian rp genes, the DNA immediately upstream of the rpL34 gene lacks the TATA box, and the rpL34 transcription initiation site is embedded in a characteristic polypyrimidine tract. The 5'-flanking DNA contained a number of cis-acting elements that potentially interact with transcription factors characterized by basic domains, zinc-coordinating DNA binding domains, helix-turn-helix motifs, and beta scaffold factors with minor groove contacts. Particularly striking was the conservation of an AP-4 binding site within 100 nucleotides upstream of the transcription initiation site in both Aal-rpL34 and Aal-rpL8 genes. Comparison of Southern hybridization signals using probes from the 5' and 3'-ends of the 5.3 kb second intron and the cDNA suggested that the Ae. albopictus rpL34 gene most likely occurs as a single expressed copy per haploid genome with restriction enzyme polymorphisms in the upstream flanking DNA and the likely presence of one or more pseudogenes.

Aedes↗

PubMed2005

Sensitive detection of deletions of one or more exons in the neurofibromatosis type 2 (NF2) gene by multiplexed gene dosage polymerase chain reaction.

Mutation detection in the neurofibromatosis type 2 (NF2) gene is challenging because when combining mutation detection methods such as single-strand conformational polymorphism and heteroduplex analysis, denaturing gradient gel electrophoresis, and direct sequencing of aberrant polymerase chain reaction (PCR) fragments only 30 to 60% of the constitutional mutations are detected. Because large deletions and complete chromosome rearrangements are also described methods such as microarray-comparative genomic hybridization and fluorescence in situ hybridization are also used. The one type of mutation often missed corresponds to deletions encompassing one or few exons. To detect this type we have developed a swift and reliable method. We perform a gene dosage analysis with two fluorescent multiplex PCR assays that amplify 15 of the 17 NF2 exons. The labeled PCR products are quantified and gene dose is calculated with respect to controls. We tested the reliability of this method with DNA from eight NF2 patients with known heterozygous NF2 deletions, eight controls and four unknown NF2 patients. In all of the patients with known heterozygous deletions we found in several exons a reduction of gene dosage to 50 to 69%. In one NF2 patient with previously unknown mutation and a severe phenotype we found the gene dosage of two exons reduced by 50% indicating a deletion of these two exons on one allele. This finding was validated by reverse transcriptase-PCR on fibroblast and schwannoma cell cultures of this patient and cDNA sequencing. Our gene dosage assay will detect deletions of one or more exons as well as gross deletions of the whole coding region of the gene. It can complement the existing screening methods because it is faster and easier.

DNA Mutational Analysis↗

PubMed2004

KIT gene deletions at the intron 10-exon 11 boundary in GI stromal tumors.

Most gastrointestinal stromal tumors (GISTs) harbor oncogenic mutations in the KIT gene, and the majority of these mutations affect the juxtamembrane domain of the kinase encoded by exon 11. Screening GISTs for KIT gene mutations is important for translational research studies and for providing prognostic information on the likelihood of tumor response to treatment with the kinase inhibitor imatinib mesylate (Gleevec). In a series of GISTs analyzed in our laboratory by a combination of denaturing HPLC and direct DNA sequencing, we identified 19 cases with KIT exon 11 deletions that included from 1 to 14 bp of intron 10 sequence and resulted in loss of the normal splice acceptor site at the beginning of exon 11. Predicted use of the next potential splice-acceptor site was confirmed by cDNA sequencing in 4 cases. Thus, the resulting mutant isoform, deletion KPMYEVQWK 550-558, was the same in all 19 cases. Only two other examples of deletions across the intron 10-exon 11 boundary have been reported, yet among 722 GISTs analyzed in our laboratories these deletions were not uncommon, accounting for 3.9% of exon 11 mutations and 2.6% of all tumors. Loss of KIT intron 10 sequences may be under-recognized if the forward primer is too close to exon 11, or if cases are examined exclusively at the cDNA level. Laboratories that offer clinical screening for KIT mutations in GI stromal tumors should be aware of this class of mutations.

Amino Acid Sequence↗

PubMed1998

Enhancer elements activate the weak 3' splice site of alpha-tropomyosin exon 2.

We have identified four purine-rich sequences that act as splicing enhancer elements to activate the weak 3' splice site of alpha-tropomyosin exon 2. These elements also activate the splicing of heterologous substrates containing weak 3' splice sites or mutated 5' splice sites. However, they are unique in that they can activate splicing whether they are placed in an upstream or downstream exon, and the two central elements can function regardless of their position relative to one another. The presence of excess RNAs containing these enhancers could effectively inhibit in vitro pre-mRNA splicing reactions in a substrate-dependent manner and, at lower concentrations of competitor RNA, the addition of SR proteins could relieve the inhibition. However, when extracts were depleted by incubation with biotinylated exon 2 RNAs followed by passage over streptavidin agarose, SR proteins were not sufficient to restore splicing. Instead, both SR proteins and fractions containing a 110-kD protein were necessary to rescue splicing. Using gel mobility shift assays, we show that formation of stable enhancer-specific complexes on alpha-tropomyosin exon 2 requires the presence of both SR proteins and the 110-kD protein. By analogy to the doublesex exon enhancer elements in Drosophila, our results suggest that assembly of mammalian exon enhancer complexes requires both SR and non-SR proteins to activate selection of weak splice sites.

Alternative Splicing↗

PubMed1991

Alternative secondary structures in the 5' exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA.

The natural splice junction of the Tetrahymena large ribosomal RNA is flanked by hairpins that are phylogenetically conserved. The stem immediately preceding the splice junction involves nucleotides that also base pair with the internal guide sequence of the intervening sequence during splicing. Thus, precursors which contain wild-type exons can form two alternative helices. We have constructed a series of RNAs where the stem-loop in the 5' exon is more or less stable than in the wild-type precursor, and tested them in both forward and reverse self-splicing reactions. The presence of a stable hairpin in ligated exon substrates interferes with the ability of the intervening sequence to integrate at the splice junction. Similarly, the presence of the wild-type hairpin in the 5' exon reduces the rate of splicing 20-fold in short precursors. The data are consistent with a competition between unproductive formation of a hairpin in the 5' exon and productive pairing of the 5' exon with the internal guide sequence. The reduction of splicing by a hairpin that is a normal feature of rRNA structure is surprising; we propose that this attenuation is relieved in the natural splicing environment.

Animals↗

PubMed1997

Murine hepatic beta-galactoside alpha 2,6-sialyltransferase gene expression involves usage of a novel upstream exon region.

ST6Gal I (beta-galactoside alpha 2,6-sialyltransferase, SiaT-1, ST6N, EC 2.4.99.1) mediates the attachment of the alpha 2,6-sialyl linkage common on N-linked glycans. Previous work suggests substantial inter-species conservation in SIAT1, the gene encoding ST6Gal I. In human and in rat, hepatic-specific SIAT1 transcription is initiated at Exon I. Here we report a surprising departure in the structural organization of the murine ST6Gal I gene. By a combination of primer extension analysis, 5'-RACE analysis, and analysis of genomic sequences, we show that the murine hepatic ST6Gal I mRNA contains a novel region 5' of Exon I. This novel sequence is encoded on a discrete upstream exon, Exon H. In contrast to human and rat hepatic ST6Gal I, the murine mRNA is transcriptionally initiated at the start of Exon H. Differential mRNA blot analysis indicates that transcripts containing Exon H sequences are preferentially expressed in liver.

Animals↗

PubMed2001

Identification of MICA alleles with a long Leu-repeat in the transmembrane region and no cytoplasmic tail due to a frameshift-deletion in exon 4.

MHC class I chain-related gene A (MICA) is located close to HLA-B gene and expressed in epithelial cells. The MICA gene is reported to be highly polymorphic as are the classical class I genes. To further assess the polymorphism in the MICA gene, we analyzed a total of 60 HLA-homozygous cells for the sequences spanning exons 2-6. In the analysis, four new MICA alleles were identified and six variations were recognized in exon 6. MICA*017, which was identified in three HLA-B57 homozygous cells (DBB, DEM and WIN), differed from MICA*002 in exon 3 and had a guanine deletion at the 3' end of exon 4. MICA*015 identified in an HLA-B45 homozygous cell (OMW) also had the same deletion that causes a frameshift mutation resulting in complete change of the transmembrane region and premature termination in the cytoplasmic tail; these alleles have a long hydrophobic leucine-rich region instead of the alanine repeat in the transmembrane region and terminate at the second position in the cytoplasmic domain. The frameshift deletion was found only in HLA-B45- or -B57-positive panels tested, suggesting a strong linkage disequilibrium between the deletion and B45 or B57. MICA*048, which was different in exon 5 from MICA*008, was identified in an HLA-B61 homozygous cell (TA21), while MICA*00901 identified in HLA-B51 homozygous cells (LUY and KT2) was distinguished from MICA*009 by exon 6.

Base Sequence↗

PubMed1996

The COL4A5 gene in Japanese Alport syndrome patients: spectrum of mutations of all exons. The Japanese Alport Network.

To determine the spectrum of mutations of the COL4A5 gene encoding type IV collagen among Japanese Alport syndrome (AS) patients, 60 unrelated patients (47 males and 13 females) from all over the country were recruited. Screening for mutations in all the exons (1 to 51) of the COL4A5 gene was carried out by PCR-SSCP analysis. A mobility shift was observed in 22 of 60 patients, and their genomic DNA were analyzed by the direct sequence method and using cloned ssDNA. Nine of these had missense mutations in the collagenous domain (in exons 39, 37, 31, 29, 28, 27, 21, 20, 19). Eight of these mutations were observed in a codon of glycine residue. Two were altered to arginine, two to valine, two to glutamic acid and two to aspartic acid. The other missense mutation was a change from isoleucine to serine in a interruption region. Five patients had small size base deletions and one had a 4 bp insertion resulting in frameshift (in exons 49, 41, 19, 14, 13). Three had a splice site mutation (in exons 49, 47, 27). One had a nonsense mutation (in exon 17). These mutations seemed to be pathogenic, but the phenotype, which includes extrarenal manifestations, can vary with respect to both expression and severity. The remaining mutations were three silent ones (in exons 19, 39, 46). In addition, major gene rearrangement seemed to be rare in Japanese AS patients.

Adult↗

PubMed1994

Isolation of genes from complex sources of mammalian genomic DNA using exon amplification.

Modifications to exon amplification have been instituted that increase its speed, efficiency and reliability. Exons were isolated from target human or mouse genomic DNA sources ranging from 30 kilobases (kb) to 3 megabases (Mb) in complexity. The efficiency was dependent upon the amount of input DNA, and ranged from isolation of an exon for every 20 kb to an exon for every 80 kb of target genomic DNA. In these studies, several novel genes and a smaller number of genes isolated previously that reside on human chromosome 9 have been identified. These results indicate that exon amplification is presently adaptable to large scale isolation of exons from complex sources of genomic DNA.

Animals↗

PubMed2005

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs.

Recent mammalian microarray experiments detected widespread transcription and indicated that there may be many undiscovered multiple-exon protein-coding genes. To explore this possibility, we labeled cDNA from unamplified, polyadenylation-selected RNA samples from 37 mouse tissues to microarrays encompassing 1.14 million exon probes. We analyzed these data using GenRate, a Bayesian algorithm that uses a genome-wide scoring function in a factor graph to infer genes. At a stringent exon false detection rate of 2.7%, GenRate detected 12,145 gene-length transcripts and confirmed 81% of the 10,000 most highly expressed known genes. Notably, our analysis showed that most of the 155,839 exons detected by GenRate were associated with known genes, providing microarray-based evidence that most multiple-exon genes have already been identified. GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes.

Algorithms↗