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At least 865 records · Page 48Linked to original sources

PubMed1995

Lineage-specific alternative splicing of the human Fc gamma RIIA transmembrane exon requires sequences near the 3' splice site.

The human Fc gamma RIIA gene produces multiple transcripts, including those with (Fc gamma RIIa1) and without (Fc gamma RIIa2) the single exon encoding the transmembrane domain (TM). Previously, a fluorescence-based RT-PCR assay showed lineage-specific differences in Fc gamma RIIA transcript ratios (Fc gamma RIIa2/Fc gamma RIIa1). The mechanism of this lineage-specific expression was investigated in this study. Differential transcript stability does not play a major role, because transcript ratios remained constant in cells with both low (K562) and high (Dami) ratios following actinomycin D treatment. Transient expression studies in K562 and Dami cells using a minigene construct containing a 5.0 kb genomic fragment including the TM exon and adjacent intron and exon sequences showed recapitulation of endogenous transcript ratios. The TM exon was efficiently spliced in by the constitutive splicing machinery in HeLa cells, an Fc gamma RIIA-negative cell line. Lineage-specific TM exon skipping was markedly diminished by two independent minigene mutations: a point mutation of the first nucleotide of the TM exon, and a five basepair intronic deletion near a putative branchpoint. These data demonstrate that cis-acting sequences in or near the TM exon 3' splice acceptor site contribute to lineage-specific differences in Fc gamma RIIA transcript ratios.

Alternative Splicing↗

PubMed1994

Exon 11 enhances insulin binding affinity and tyrosine kinase activity of the human insulin proreceptor.

Data presented here show that there are significant differences in the insulin binding affinity and the tyrosine kinase activity of the insulin proreceptor isoforms which contain or lack exon 11. The exon 11(+) proreceptor does not show significant variations from the mature processed insulin receptor and has only a 3- to 4-fold reduced affinity for insulin. In contrast, the exon 11(-) proreceptor showed a markedly reduced insulin binding (25- to 50-fold less) when assayed on intact cells. Upon solubilization of the cells, exon 11(-) proreceptor bound insulin with somewhat higher affinity. Mild trypsin treatment of the cells expressing either isoform of the insulin proreceptor restored insulin binding to near-normal levels. Analysis of tyrosine kinase activity revealed that the exon 11(+) proreceptor required somewhat higher concentrations of insulin than the mature processed receptor to achieve maximal autophosphorylation. The exon 11(-) proreceptor failed to fully phosphorylate even at 10(-6) M insulin. Thus, the presence or absence of this short sequence of 12 amino acids affects the folding and/or conformation of the proreceptor so as to confer altered binding of insulin. We suggest that in the absence of exon 11 the proreceptor assumes a strained conformation that disrupts the insulin binding site. Cleavage of the proreceptor at the alpha-beta-subunit junction then allows the alpha-subunit to achieve its normal binding conformation.

Affinity Labels↗

PubMed1993

In vitro analysis of bovine growth hormone pre-mRNA alternative splicing. Involvement of exon sequences and trans-acting factor(s).

Bovine growth hormone (bGH) pre-mRNA is alternatively spliced, resulting in retention of the last intron (intron D) in a fraction of the cytosolic bGH mRNA. To study the mechanism of this alternative splicing event, we examined the splicing of bGH pre-mRNA in vitro. The splicing of bGH intron D in vitro required a 115-base pair segment of exon 5, reflecting the positive influence of exon sequences observed in transfected cells. No detectable spliceosome complex formation was observed using bGH pre-mRNA containing the 115-base pair deletion in exon 5. The in vitro splicing of the wild type bGH pre-mRNA was inhibited by the addition of RNA containing the 115-nucleotide exon sequence, but not by nonspecific RNAs. UV irradiation of the in vitro splicing reaction resulted in specific cross-linking of a 35-kDa protein(s) to the 115-nucleotide bGH exon sequence. These results suggest that terminal exon sequences are required at an early step of spliceosome complex formation and are consistent with a mechanism in which saturable, trans-acting factor(s) bind to these exon sequences to activate spliceosome complex formation and splicing of bGH intron D.

Alternative Splicing↗

PubMed1996

Restricted patterns of CD44 variant exon expression in human papillary thyroid carcinoma.

CD44 is a polymorphic family of cell surface proteoglycans and glycoproteins implicated in cell-cell and cell-matrix adhesion interactions, cell migration, and tumor metastasis. CD44 exists as a standard form and as multiple isoforms arising from alternative splicing of variant exons (termed v1-v10) encoding parts of the extracellular domain. We demonstrated previously that papillary thyroid carcinomas exhibit aberrant patterns of alternative CD44 mRNA splicing (G. Ermak et al., Cancer Res., 55: 4594-4598, 1995). In the present report, we use reverse transcription-PCR using a new high-performance polymerase formulation (Ex Taq; TaKaRa Shuzo Co., Ltd., Otsu, Japan) , followed by Southern hybridization, and demonstrate that alternative exon usage in papillary thyroid carcinomas is restricted primarily to exons v6, v7, v8, v9, and v10, with weak expression of v3. Expression of v8 is tightly linked to v9 and closely related to v10 expression. Also, v6 and v7 expression are closely related. Papillary thyroid cancers exhibit a marked increase in specific mRNA species containing combinations of exons v6 to v10. Several isoforms found in papillary cancers are not detectable in histologically normal tissue derived from the corresponding contralateral thyroid lobes. Examples include a 750-bp v6- and v7-containing PCR product and a 650-bp v8- and v9- containing PCR product. Finally, a novel 530-bp PCR product was discovered and shown to contain a subsegment from exon 4 joined to a subsegment of exon 13 (v8), followed by the complete sequence of exons 14 (v9) and 15 (v10). This novel isoform was present in both the papillary cancers and contralateral tissues. In conclusion, papillary thyroid cancers exhibit specific patterns of aberrant alternative CD44 splicing, distinguishing them from histologically normal thyroid tissue.

Alternative Splicing↗

PubMed1996

A novel nonsense mutation associated with an exon skipping in a patient with hereditary protein S deficiency type I.

The genetic defect in a patient with hereditary type I protein S (PS) deficiency was investigated. All the exons and intron-exon junctions of the patient's PS gene were amplified by PCR and subjected to heteroduplex screening. Only the PCR product of exon 4 revealed heteroduplex bands. A novel nonsense mutation, Ser62 (TCA) to Stop (TGA) was found in exon 4. RT-PCR detected the aberrant mRNA in the patient's platelets, which was markedly reduced in amount and lacked the region of exon 4, suggesting that the nonsense mutation affected the mutated mRNA metabolism and induced exon skipping. The skipping of exon 4 causes an in-frame deletion of 29 amino acids which just construct the thrombin-sensitive region of the PS molecule. The loss of such an important domain as well as the quantitative decrease in the mutated mRNA appear to be responsible for the type I PS deficiency in this patient.

Exons↗

PubMed1997

A highly stable duplex structure sequesters the 5' splice site region of hnRNP A1 alternative exon 7B.

Exon 7B in the hnRNP A1 pre-mRNA is alternatively spliced to yield A1 and A1(B), two proteins that differ in their ability to modulate 5' splice site selection. Sequencing the murine intron downstream of exon 7B revealed the existence of several regions of similarity to the corresponding human intron. In vitro splicing assays indicate that an 84-nt region (CE6IO) decreases splicing to the proximal 5' splice site in a pre-mRNA carrying the 5' splice sites of exon 7 and 7B. In vivo, the CE6IO element promotes exon 7B skipping in pre-mRNAs expressed from a mini-gene containing the hnRNP A1 alternative splicing unit. Using oligonucleotide-targeted RNase H cleavage assays, we provide support for the existence of highly stable base pairing interactions between CE6IO and the 5' splice site region of exon 7B. Duplex formation occurs in naked pre-mRNA, resists incubation in splicing extracts, and is associated with a reduction in the assembly of U1 snRNP-dependent complexes to the 5' splice site of exon 7B. Our results demonstrate that pre-mRNA secondary structure plays an important role in promoting exon 7B skipping in the A1 pre-mRNA.

Alternative Splicing↗

PubMed1997

Immortalization of primary epithelial cells by E1A 12S requires late, second exon-encoded functions in addition to complex formation with pRB and p300.

Immortalization of primary cells is an early and important event in multistep tumorigenesis and is itself a multistep process. Adenovirus E1A 12S encodes an oncoprotein that can rescue cells from senescence and overcome apoptosis, leading to their immortalization. Five regions of 12S, located in both exons, are required for immortalization. Two regions in the first exon are necessary to activate the cell cycle, increase the number of population doublings, and overcome the M1 stage of mortality. However, extension of life span requires overcoming crisis or M2, which can be accomplished by the expression of the second exon. Several cellular proteins associate with the peptide encoded by the first exon of 12S including pRB, p107, p130, and p300. The importance of pRB-E1A and p300-E1A complexes in transformation is well established; however, their roles in 12S-mediated immortalization remain undefined. Results obtained from the present study using a panel of second exon immortalization-defective mutants demonstrate that formation of pRB-E1A and p300-E1A complexes is insufficient for immortalization of primary cells. We further demonstrate that the expression levels of another tumor suppressor protein, p53, also do not correlate with the inability of the mutants to immortalize. Thus, mutations in the second exon of 12S do not affect the early steps in the immortalization pathway. The second exon mutants are defective in performing a late function in immortalization, involving the reactivation of the cell cycle, indicating that it is a crucial event in immortalization.

Adenovirus E1A Proteins↗

PubMed1998

A directly spliced exon 10-containing CD44 variant promotes the metastasis and homotypic aggregation of aggressive non-Hodgkin's lymphoma.

Variants of the CD44 cell-surface adhesion molecule include additional sequences encoded by combinations of exons from the membrane proximal domain (exons 6-14). Preliminary studies suggest that these additional variable membrane proximal sequences may alter the ligand specificity, glycosylation, and biologic function of CD44. In earlier studies, we found that primary extranodal and widely disseminated aggressive non-Hodgkin's lymphomas (NHLs) and normal activated B cells expressed a directly spliced exon 10-containing variant (CD44ex10), whereas normal resting B cells expressed larger exon 10-containing variants (CD44ex10-14 and CD44ex7-14). To obtain additional information regarding the function of exon 10-containing CD44 variants in aggressive NHL, we generated aggressive NHL transfectants that expressed CD44ex10, CD44ex10-14, CD44ex7-14, the standard CD44 isoform (CD44H), or vector alone, and evaluated the local tumorogenicity, aggregation, and metastatic potential of these transfectants. CD44ex10 aggressive NHL transfectants were more likely to cause local tumor formation in nude mice than transfectants expressing the larger exon 10-containing variants, CD44H, or vector alone. In addition, cell suspensions derived from CD44ex10 local tumors exhibited far greater homotypic aggregation than those obtained from other CD44 or vector-only local tumors. In nude mice that received CD44ex10 transfectants, distant metastases were also significantly more likely to develop than in animals that were given either the CD44ex10-14, CD44ex7-14, CD44H, or vector-only transfectants. These data provide the first evidence that the directly spliced exon 10-containing CD44 variant (CD44ex10) has a unique biologic function in aggressive NHL.

Alternative Splicing↗

PubMed1984

Characterization of bovine keratin genes: similarities of exon patterns in genes coding for different keratins.

Four different genomic clones which contain the genes coding for epidermal keratins Ia (mol. wt. approximately 68 000), Ib (68 000), III (60 000) and VIb (54 500) have been selected using cDNA probes and identified by hybrid-selection translation. The genes vary considerably in length, primarily due to differences in intron sizes: keratin Ia, 9.3 kb (approximately 2.55 kb total exons); keratin Ib, 6.0 kb (2.25 kb exons); keratin III, 6.0 kb (2.2 kb exons); keratin VIb, 4.4 kb (1.85 kb exons). The genes for all three representatives of the basic (type II) cytokeratin subfamily, i.e., keratins Ia, Ib and III, contain eight introns of variable sizes (0.1-1.8 kb) and their exon patterns are very similar. The gene coding for keratin VIb, a representative of the acidic (type I) subfamily, contains seven introns, and the size pattern of its five innermost exons closely resembles that of the genes of the type II keratins. Most of the introns are located in regions coding for the alpha-helical cores of these proteins. Mapping of the intron positions by the S1 nuclease technique and sequencing of some exon-intron boundaries has revealed that some of the introns of all four keratin genes have similar positions to each other and to those of the hamster vimentin gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

Population haplotypes of exon ORF15 of the retinitis pigmentosa GTPase regulator gene in Germany : implications for screening for inherited retinal disorders.

BACKGROUND: Mutations in exon ORF15 of the retinitis pigmentosa GTPase regulator gene (RPGR) within chromosomal region Xp21.1 are a significant cause of a number of retinal disorders. The high mutation rate is ascribed to the highly repetitive, purine-rich tracts within the exon ORF15 sequence. Importantly, all exon ORF15 mutations observed to date represent protein-truncating mutations (nonsense and frameshift mutations). Because of its repetitive motifs, mutation screening of the hot-spot region by direct DNA sequencing is a technically challenging task. METHODS: We devised a screening strategy for exon ORF15 mutations that reserves DNA sequencing for precise sizing and base-order assessment of detected mutations. The screening strategy is based on a PCR/restriction fragment length polymorphism (RFLP) analysis of exon ORF15 and comparison with population-specific RFLP haplotypes. The latter were constructed from PCR/RFLP analysis of DNA samples from 100 healthy German male individuals. Mutational alterations of normal RFLP haplotype patterns were predicted. RESULTS: Six distinct RFLP haplotypes (founder alleles H1-H6) were observed with frequencies ranging from 2% to 63%. All natural variations of exon ORF15 were in-frame alterations ranging in size between 3bp and 36bp. Prediction of mutation-specific RFLP patterns indicated a high detection rate of mutations. CONCLUSION: A new strategy has been developed using routine protocols for mutation screening of difficult-to-sequence, highly repetitive exon ORF15 of the RPGR gene in a German population.

Base Sequence↗

PubMed1986

Complete nucleotide sequence of the fast skeletal troponin T gene. Alternatively spliced exons exhibit unusual interspecies divergence.

The continuous nucleotide sequence of the rat fast skeletal muscle troponin T gene is reported, complementing the previous determinations of its structural organization and its capacity to encode multiple isoforms via alternative RNA splicing. Canonical promoter elements, as well as consensus sequences that may be involved in the 3' processing of the primary transcript, are present. All exons are flanked by conventional donor and acceptor splice sites, which can hybridize to U1 RNA. Extensive computer-assisted analyses of the genomic sequence do not reveal cis elements that unambiguously distinguish alternative from constitutive exons. Local RNA secondary structures can be predicted, however, that sequester exons or their splice sites in stem-and-loop formations, and which may also pair with small nuclear RNAs. These interactions might, in theory, contribute to differential exon usage. The structural features of exon organization that characterize this rat skeletal gene are closely conserved in the chicken cardiac troponin T gene, but the former exhibits a more diversified capacity for differential splicing. Implications for the mechanisms of alternative RNA splicing are considered. Comparisons of troponin T amino acid sequences among several species reveal striking dissimilarities, in contrast to the otherwise highly conserved contractile proteins. These divergences involve entire peptide subsegments and are concentrated in the same domains as are encoded by alternatively spliced exons, suggesting that exon shuffling may have contributed to the evolution of troponin T.

Amino Acid Sequence↗

PubMed1995

The immune response to a subdominant epitope in myelin basic protein exon-2 results in immunity to intra- and intermolecular dominant epitopes.

Experimental autoimmune encephalomyelitis was induced in SJL/J mice by adoptive transfer of a MBP exon-2 peptide-specific T cell line. The T cell line, when tested for antigen specificity, reacted strongly with exon-2 peptide, but not with MBP peptides pAc1-11, p43-88, p89-101 or PLP p139-151. The specificity of splenic or lymph node T cells isolated from mice with acute or first relapse EAE induced by adoptive transfer of the exon-2-specific T cell line was identical to the transferred line. Splenocytes or lymphocytes isolated from mice at the second relapse were reactive with MBP p43-88, p89-101 and PLP p139-151 in addition to exon-2 peptide and MBP peptide Ac1-11. T cell lines selected by culture with MBP exon-2 peptide or PLP p139-151 from splenic cells from mice with relapsing EAE were weakly encephalitogenic; however, T cell lines selected from the same mice with MBP pAc1-11 were not encephalitogenic. T cells from the exon-2 and p139-151 T cell lines primed recipients for rapid onset severe EAE, whereas the pAc1-11 T cell line did not. T cells from the exon-2-specific line did not express V beta 17a+ TCR; however, peptide-specific T cell lines derived from the spleens of relapsing animals did express this TCR gene segment providing direct evidence of recruitment and sensitization of recipient T cells.

Amino Acid Sequence↗

PubMed2001

Polymorphisms at the five exons of the growth hormone gene in the algarvia goat: possible association with milk traits.

The present preliminary study attempts to establish associations between milk production traits and genetic polymorphisms at the GH gene in the Algarvia goat. The DNA of 108 goats of the indigenous Portuguese Algarvia breed was evaluated. Single-strand conformation polymorphisms (SSCP) were identified at the five exons of the goat growth hormone (gGH) gene. Two conformational patterns were found in each of exons 1 and 2, four in exon 3, six in exon 4 and five in exon 5. An association between these SSCP patterns with milk, fat and protein production, and fat and protein content was examined. Patterns F/F of exon 4 and A/A of exon 5 were positively associated with milk production (P<0.05). The results demonstrated that the gGH gene could be exploited as a candidate gene for marker-assisted selection in goat breeds.

Journal Article↗

PubMed2002

An exonic mutation of the GH-1 gene causing familial isolated growth hormone deficiency type II.

A heterozygous base change was identified in exon 3 of the growth hormone (GH)-1 gene in a Japanese family with autosomal dominant GH deficiency. All of the patients from this family had a heterozygous G to T transversion at the first 5'-site nucleotide of exon 3. Analysis of the GH-1 cDNA, synthesized from lymphoblasts of the patients, revealed an abnormal shorter transcript as well as a normal-sized transcript. Direct sequencing of this abnormal transcript showed that the transcript completely lacked exon 3. In familial isolated GH deficiency (IGHD) type II, several heterozygous mutations have been reported at the donor splice site in intron 3 of the GH-1 gene or inside intron 3, which causes aberrant GH messenger RNA splicing, resulting in the deletion of exon 3. This deletion causes a lack of amino acid residues 32-71 in the mature GH protein. This mutant GH is well-known to exert a dominant negative effect on the secretion of mature normal GH protein. Thus, in the subject family, a heterozygous G-to-T transversion at the first nucleotide of the exon 3 deletes exon 3 in mature GH mRNA and causes GH deficiency. The present authors suggest that the first nucleotide of exon 3 is critical for the splicing of GH-1 mRNA.

Alternative Splicing↗

PubMed2006

An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.

Numerous disease-associated point mutations exert their effects by disrupting the activity of exonic splicing enhancers (ESEs). We previously derived position weight matrices to predict putative ESEs specific for four human SR proteins. The score matrices are part of ESEfinder, an online resource to identify ESEs in query sequences. We have now carried out a refined functional SELEX screen for motifs that can act as ESEs in response to the human SR protein SF2/ASF. The test BRCA1 exon under selection was internal, rather than the 3'-terminal IGHM exon used in our earlier studies. A naturally occurring heptameric ESE in BRCA1 exon 18 was replaced with two libraries of random sequences, one seven nucleotides in length, the other 14. Following three rounds of selection for in vitro splicing via internal exon inclusion, new consensus motifs and score matrices were derived. Many winner sequences were demonstrated to be functional ESEs in S100-extract-complementation assays with recombinant SF2/ASF. Motif-score threshold values were derived from both experimental and statistical analyses. Motif scores were shown to correlate with levels of exon inclusion, both in vitro and in vivo. Our results confirm and extend our earlier data, as many of the same motifs are recognized as ESEs by both the original and our new score matrix, despite the different context used for selection. Finally, we have derived an increased specificity score matrix that incorporates information from both of our SF2/ASF-specific matrices and that accurately predicts the exon-skipping phenotypes of deleterious point mutations.

Alternative Splicing↗

PubMed1985

Structure and exon to protein domain relationships of the mouse carbonic anhydrase II gene.

We have isolated a cosmid clone containing the entire mouse (YBR strain) carbonic anhydrase (CA) II gene in 38 kilobase pairs of genomic DNA. The gene was found to be composed of seven exons and six introns. A TATA box (TATAAAA) and a possible CCAAT box (CCACT) have been located beginning 92 and 142 base pairs, respectively, upstream from the initiation codon ATG. When the regions encoded by exons and protein domains are examined, all but 1 of the 30 putative active site residues are encoded by four exons: exons 2 and 3 mainly code for hydrophilic residues and exons 4 and 6 mostly hydrophobic residues. Two intron splice positions, one between the codons for Glu-116 and Leu-117 and the other interrupting the codon for Gly-143, are located at the bottom of the active site cavity, and the former separates two of the three histidine residues forming ligands to the active site zinc ion. The other four splice sites map to the exterior of the molecule. Thus, except for the possible association of the 29 active site residues encoded by four exons, no obvious correspondence is seen between the regions coded by exons and the functional or secondary structural domains of the mouse CA II molecule. During this study, the possible basis for the two electrophoretic types, CA IIa and CA IIb, of inbred mouse strains was detected as a Gln/His interchange at position 38.

Amino Acid Sequence↗

PubMed1989

A human immunoglobulin IGHG3 allele (Gmb0,b1,c3,c5,u) with an IGHG4 converted region and three hinge exons.

The five human IGHG genes consist of three constant domain exons plus one of or four hinge exon(s), the quadruplicated hinge region being characteristic of the IGHG3 gene. Besides this structural difference, the IGHG genes are polymorphic, as demonstrated by the restriction fragment length polymorphism and, at the protein level, by the Gm allotypic antigenic determinants. In this paper, we report the sequence of the G3m(b0, b1, c3, c5,u) IGHG3 allele, typical of the Black African populations and of populations with Negroid admixture, found in a homozygous Tunisian designated as LAT. We demonstrate that this G3 allele contains only three hinge exons instead of four (the probable result of an unequal crossing over) and that IGHG3 genes with triplicated hinge exons (and therefore encoding shorter gamma 3 chains) are present in healthy individuals from different populations. Moreover, we show that the LAT G3m (b0, b1, c3, c5, u) coding sequence results from the conversion, in the CH3 exon, of the G3m (b0, b1, b3, b4, b5, u, v) allele, the most frequent IGHG3 gene in the Negroid populations, by the homologous region of a IGHG4 gene. The structural features of the LAT IGHG3 allele, which are the lack of one hinge exon and its conversion by the IGHG4 gene, demonstrate that both crossing-over and gene conversion events occur in the evolution of the human IGHG genes.

Alleles↗

PubMed2025

Rescue of a panel of Hemophilia A-causing 5'ss splicing mutations by unique Exon-specific U1snRNA variants.

BACKGROUND: Aberrant mRNA splicing is a well-established pathogenic mechanism for human disease, but its real impact is hardly predictable and underestimated. Splicing can be therefore modulated for therapeutic purposes, and splicing-switching molecules are in clinics for some diseases. Here, conscious that over 10% of all pathogenic mutations occurs at 5'ss, we aimed at characterizing and rescuing nine 5'ss mutations in three models of defective F8 exons whose skipping would lead to factor VIII (FVIII) deficiency (Hemophilia A), the most frequent coagulation factor disorder. METHODS: HEK293T cells were transfected with F8 minigene variants, alone or with engineered U1 small nuclear RNAs (U1snRNAs), and splicing patterns analysed via RT-PCR. RESULTS: All 5'ss mutations induced exon skipping, and the proportion of correct transcripts, not predictable by computational analysis, was consistent with residual FVIII levels in patients. For each exon we identified a unique engineered U1snRNAs, either compensatory or Exon Specific (ExSpeU1), able to rescue all mutations. Overall, ExSpeU1s were more effective than compensatory U1snRNAs, particularly in the defective exons 6 and 22. CONCLUSIONS: Data highlight the importance of splicing assays to elucidate genotype-phenotype relationships and proved the correction efficacy of ExSpeU1s for each targeted defective F8 exon, thus expanding their translational potential for HA.

Humans↗