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PubMed1986

Evolution of the fibronectin gene. Exon structure of cell attachment domain.

Genomic DNA coding for human fibronectin was identified from a human genomic library by screening with a cDNA clone that specifies the cell attachment domain in human fibronectin. Two clones which together provided more than 22 kilobase pairs of the fibronectin gene were isolated. The exons in this region correspond to approximately 40% of the coding region in the fibronectin gene. They code for the middle region of the polypeptide which consists of homologous repeating segments of about 90 amino acids called type III homologies. Nucleotide sequence of the portion of the gene corresponding to the cell attachment domain showed that the Arg-Gly-Asp-Ser cell attachment site is encoded within a 165-base pair exon. This exon, together with a 117-base pair exon codes for a homology unit. Analysis of the exon/intron organization in some of the neighboring homology units indicated a similar 2-exon structure. An exception to this pattern is that a single large exon codes for a type III homology unit that, due to alternative mRNA splicing, exists in some but not all fibronectin polypeptides. The introns separating the coding sequences for the type III homology units are located in conserved positions whereas the introns that interrupt the coding sequence within the units are in a variable position generating variations in the size of the homologous exons. This exon/intron organization suggests that the type III homology region of the fibronectin gene has evolved by a series of gene duplications of a primordial gene consisting of two exons. Specification of one of these homology units to the cell attachment domain has occurred within this exon/intron arrangement.

Base Sequence↗

PubMed2002

Polymorphisms for interleukin 1 beta exon 5 and interleukin 1 receptor antagonist in Taiwanese children with febrile convulsions.

OBJECTIVE: To investigate whether interleukin 1 beta (IL-1 beta) exon 5 and IL-1 receptor antagonist (IL-1Ra) gene polymorphisms can be used as markers of susceptibility to febrile convulsions in children. METHODS: Children were divided into 2 groups: those with febrile convulsions (group 1; n = 51) and normal control subjects (group 2; n = 83). Polymorphisms for IL-1 beta exon 5 and IL-1Ra gene polymorphisms were detected by polymerase chain reaction. Genotypes and allelic frequencies for IL-1 beta exon 5 and IL-1Ra gene polymorphisms in both groups were compared. RESULTS: Genotype and allele frequencies for IL-1 beta exon 5 in both groups were not significantly different. Proportions of E1 homozygotes and E1/E2 heterozygotes for IL-1 beta exon 5 were 50 (98.1%) and 1 (1.9%), respectively, in group 1 and 82 (98.8%) and 1 (1.2%), respectively, in group 2. Frequencies of alleles E1 and E2 for IL-1 beta exon 5 were 101 (99.0%) and 1 (1.0%), respectively, in group 1 and 165 (99.4%) and 1 (0.6%), respectively, in group 2. Genotype proportions and allele frequencies for IL-1Ra between groups were significantly different. Proportions of genotypes I/I and I/II for IL-1Ra were 49 (96.1%) and 2 (3.9%) in group 1 and 69 (83.1%) and 14 (16.9%) in group 2. Frequencies of alleles I and II for IL-1Ra were 100 (98.0%) and 2 (2.0%) in group 1 and 152 (91.6%) and 14 (8.4%) in group 2. CONCLUSIONS: The IL-1Ra allele I is associated with a higher susceptibility to febrile convulsion, which may become a useful marker for predicting the development of febrile convulsions. The IL-1 beta exon 5 gene polymorphisms are not a useful marker for predicting the susceptibility to febrile convulsions.

Case-Control Studies↗

PubMed1996

Delineation of the Marfan phenotype associated with mutations in exons 23-32 of the FBN1 gene.

Marfan syndrome is a dominantly inherited connective tissue disorder with a wide range of phenotypic severity. The condition is the result of mutations in FBN1, a large gene composed of 65 exons encoding the fibrillin-1 protein. While mutations causing classic manifestations of Marfan syndrome have been identified throughout the FBN1 gene, the six previously characterized mutations resulting in the severe, perinatal lethal form of Marfan syndrome have clustered in exons 24-32 of the gene. We screened 8 patients with either neonatal Marfan syndrome or severe cardiovascular complications of Marfan syndrome for mutations in this region of the gene. Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. This analysis documented mutations in exons 25-27 of the FBN1 gene in 6 of these patients. These results, taken together with previously published FBN1 mutations in this region, further define the phenotype associated with mutations in exons 24-32 of the FBN1 gene, information important for the development of possible diagnostic tests and genetic counseling.

Base Sequence↗

PubMed1998

Identification of a new heterozygous point mutation in the COL1A2 gene leading to skipping of exon 9 in a patient with joint laxity, hyperextensibility of skin and blue sclerae. Mutations in brief no. 166. Online.

A heterozygous deletion of exon 9 in the COL1A2-mRNA of a patient with symptoms of both the Ehlers-Danlos-Syndrome and the Osteogensis Imperfecta is described. In the genomic DNA of the patient, exon 9 is homozygously present. We identified a novel heterozygous point mutation in the splice donor site of intron 9, leading to a G-->A substitution in position +5. This mutation leads to heterozygous skipping of exon 9 in the COL1A2-mRNA of this patient. The deletion results in a shortened (by 18 amino acids) but in frame 12(1) chain, which probably leads to the formation of abberantly processed triple helices.

Alternative Splicing↗

PubMed1998

A point mutation within CD45 exon A is the cause of variant CD45RA splicing in humans.

The leukocyte common antigen (CD45) is alternatively spliced, generating various isoforms expressed on hemopoietic cells. The splicing pattern of CD45 in T cells is altered in some individuals who show abnormal expression of high molecular weight isoforms containing exon A. The variant splicing pattern was shown to be associated with heterozygosity for a silent point mutation within CD45 exon A. This C to G transition is located 77 nucleotides downstream of the splice acceptor junction of exon A (198 bp total length). Here we report that this mutation is the cause of abnormal splicing. To isolate the mutant gene, somatic cell hybrids of lymphocytes with a CD45 splicing defect and a mouse lymphoid line were produced and clones expressing different isoforms of CD45 were isolated. Expression of the high molecular weight isoform containing exon A was associated with the mutation within exon A. All hybrids expressing the low molecular weight isoforms lacking exon A contained the normal allele of CD45 only. In addition, minigenes including this mutation were constructed and transfected into various cell lines (COS-7, HeLa, CHO). Semi-quantitative reverse transcription polymerase chain reaction showed an increase of more than tenfold in splicing to CD45RA (concomitant with a decrease in splicing to CD45RO) when compared with the normal minigene. Taken together, these results demonstrate a causal relationship between the mutation in CD45 exon A and the variant splicing pattern observed. The involvement of trans-acting splicing factors that interact with this region of CD45 pre-mRNA is currently under investigation.

Alleles↗

PubMed1996

Three novel mutations of the NF1 gene detected by temperature gradient gel electrophoresis of exons 5 and 8.

We screened a total of 100 unrelated patients with neurofibromatosis type 1 (NF1) for mutations on exons 5 and 8 of the NF1 gene using temperature gradient gel electrophoresis (TGGE). Careful interpretation of exon 5 TGGE patterns was necessary due to interference by an exonic polymorphism. Three novel mutations were identified: a stop mutation in exon 5 (Q239X) caused by a C-->T transition at cDNA nucleotide position 715, a transition at the invariant G of the splice acceptor site in the intron 4c (G655-1A), and a transversion at the invariant G of the splice donor site in intron 8 (G1185 + 1T). Analysis of mRNA revealed the predicted abnormal splice products. While skipping of exon 5 causes a shift in the reading frame with a premature stop codon downstream in the middle of exon 6, skipping of exon 8 leads to an in-frame deletion with the predicted protein product being shortened by 41 amino acids.

Electrophoresis, Polyacrylamide Gel↗

PubMed1993

Homology-mediated recombination between type I collagen gene exons results in an internal tandem duplication and lethal osteogenesis imperfecta.

It has been proposed that the structure of the exons that encode the triple helical domain of the fibrillar collagen genes arose by repeated tandem duplication of an ancestral unit exon. Because these exons encode a repeat motif [(Gly-X-Y)n], sequence homology between exons may have driven the recombinational process. We have characterized a tandem duplication mutation within a COL1A1 allele of type I collagen from an infant with the lethal form of osteogenesis imperfecta. The structure of the mutation is consistent with the occurrence of an unequal crossover within a 15 base pair region of sequence identity between exons 14 and 17 of the COL1A1 gene. The recombination produced a new 81 base pair 17/14 hybrid exon and complete duplication of exons 15 and 16. The sequence implies duplication of 60 amino acid residues within the triple helical domain with preservation of the Gly-X-Y repeat. These data suggest that a recombinational mechanism that explains the hypothetical evolutionary process is active in cells, but the lethal effect of this mutation raises questions about the role of these events in creating new structures for polymeric proteins.

Amino Acid Sequence↗

PubMed2007

Low proportion of whole exon deletions causing phenylketonuria in Denmark and Germany.

Phenylketonuria (PKU) is an autosomal recessive genetic disorder caused by mutations of the gene encoding phenylalanine hydroxylase (PAH). More than 500 different PAH mutations have been identified and about 90% of these are single base mutations. Although the identification rate of the PAH mutations is generally very high, some variants remain unidentified. A fraction of these mutations are the result of genomic deletions or duplications, which are not recognized with standard PCR-based methods. Here we present the results of exon deletion or duplication analysis in a total of 34 families, in which two mutations had not been identified using conventional diagnostic screening techniques. Using multiplex ligation-dependent probe amplification (MLPA), we found a deletion covering exon 1 and exon 2 (c.1-?_168+?del) in one patient, a deletion of exon 3 (c.169-?_352+?del) in four patients, and a deletion of exon 5 (c.442-?_509+?del) in two patients. A deletion was thus detected in about 20% (7/34) of the families tested. Out of a combined cohort of 570 independent PKU patients from Denmark and Germany, exon deletions were identified in a total of four patients. The estimated allelic frequency of exon deletions in PKU patients in these two populations is therefore below 0.5%.

Cohort Studies↗

PubMed1991

Adenosine deaminase deficiency due to heterozygous abnormality consisting of a deletion of exon 7 and the absence of enzyme mRNA.

An adenosine deaminase (ADA;EC 3.5.4.4)-deficient B lymphoblastoid cell line BADO5 derived from a Japanese patient with severe combined immunodeficiency disease and two B lymphoblastoid cell lines, BAMO5 from his mother and BAFO5 from his father, were characterized. To identify mutations affecting ADA activity, we prepared cDNAs to ADA mRNAs of the BADO5 cell line for nucleotide sequencing. Sequence analysis of one of the BADO5 ADA cDNA clones revealed deletion of exon 7, and one point mutation of base 629 from G to A that did not affect the amino acid sequence. All clones of the BADO5 cell line so far examined showed the absence of exon 7 by Southern blotting analysis. Ribonuclease protection assay with an RNA probe spanning from exon 5 to exon 11 showed that the BADO5 ADA mRNA had a deletion of exon 7, the BAMO5 mRNA had normal length, and the BAFO5 mRNA had two species with a deletion of exon 7 and with normal length. Consequently, the patient's ADA genes resulted from one allele of the BAMO5 ADA gene that did not produce a detectable mRNA, and the other allele of the BAFO5 ADA gene producing an aberrant mRNA without exon 7.

Adenosine Deaminase↗

PubMed2004

Towards a therapeutic inhibition of dystrophin exon 23 splicing in mdx mouse muscle induced by antisense oligoribonucleotides (splicomers): target sequence optimisation using oligonucleotide arrays.

BACKGROUND: The activity of synthetic antisense oligonucleotides (splicomers) designed to block pre-mRNA splicing at specific exons has been demonstrated in a number of model systems, including constitutively spliced exons in mouse dystrophin RNA. Splicomer reagents directed to Duchenne muscular dystrophy (DMD) RNAs might thus circumvent nonsense or frame-shifting mutations, leading to therapeutic expression of partially functional dystrophin, as occurs in the milder, allelic (Becker) form of the disease (BMD). METHODS: Functional and hybridisation array screens have been used to select optimised splicomers directed to exon 23 of dystrophin mRNA which carries a nonsense mutation in the mdx mouse. Splicomers were transfected into cultured primary muscle cells, and dystrophin mRNA assessed for exon exclusion. Splicomers were also administered to the muscles of mdx mice. RESULTS: Oligonucleotide array analyses with dystrophin pre-mRNA probes revealed strong and highly specific hybridisation patterns spanning the exon 23/intron 23 boundary, indicating an open secondary structure conformation in this region of the RNA. Functional screening of splicomer arrays by direct analysis of exon 23 RNA splicing in mdx muscle cultures identified a subset of biologically active reagents which target sequence elements associated with the 5' splice site region of dystrophin intron 23; splicomer-mediated exclusion of exon 23 was specific and dose-responsive up to a level exceeding 50% of dystrophin mRNA, and Western blotting demonstrated de novo expression of dystrophin protein at 2-5% of wild-type levels. Direct intramuscular administration of optimised splicomer reagents in vivo resulted in the reappearance of sarcolemmal dystrophin immunoreactivity in > 30% of muscle fibres in the mdx mouse CONCLUSIONS: These results suggest that correctly designed splicomers may have direct therapeutic value in vivo, not only for DMD, but also for a range of other genetic disorders.

Alleles↗

PubMed2000

A novel cryptic exon in intron 2 of the human dystrophin gene evolved from an intron by acquiring consensus sequences for splicing at different stages of anthropoid evolution.

The dystrophin gene, which is mutated in Duchenne muscular dystrophy, is thus the largest human gene. A full spectrum of splicing of the dystrophin transcript has not been elucidated yet, though more than 10 alternative splicings have been identified in the 5' region of the dystrophin gene. In this study, two novel dystrophin transcripts containing a 140-nucleotide insertion precisely between exons 2 and 8 or between exons 2 and 18 were identified in skeletal muscle. The genomic region corresponding to and surrounding this 140-nucleotide sequence was sequenced to reveal that the insertion possessed a branch point and both acceptor and donor splice site consensus sequences perfectly. Therefore, the 140-bp insertion sequence was considered to be a novel exon. The novel exon was mapped to intron 2 and was designated exon 2a. Reverse-transcription PCR screening for transcripts containing exon 2a in 12 human tissues revealed its presence in 3 of them, including skeletal muscle. Phylogenetic studies disclosed that exon 2a evolved from intron DNA by the progressive acquisition of nucleotide substitutions in ancestral hominoids.

Animals↗

PubMed1993

Origin of fetal troponin T: developmentally regulated splicing of a new exon in the fast troponin T gene.

We have identified a new exon in the fast troponin T (TnT) gene whose alternative splicing is developmentally regulated. In previous studies three novel isoforms of TnT were identified in fetal and neonatal rabbit skeletal muscles (Briggs et al., 1990, Dev. Biol. 140, 253-260). These proteins are recognized by an antibody against fast TnT, but no combination of the previously identified exons could explain their protein chemical properties. To determine whether an additional exon is present in the fast TnT gene, we have cloned and sequenced cDNAs from fetal rabbit muscle RNA. Reverse transcription coupled to PCR was used with primers from conserved regions of the fast TnT sequence that span the 5' alternatively spliced exons. Sequences were obtained for each of the fetal TnTs. All included known fast TnT coding sequences plus an additional 36 nucleotides between exons 8 and 9. The peptide predicted from this sequence is highly acidic and accounts for the chemical properties of the fetal proteins. Similar experiments analyzing neonatal rat TnT cDNAs identified an homologous sequence, and comparison with the genomic sequence revealed that it is encoded by a single exon. Thus, fetal TnTs are generated from the fast TnT gene by the inclusion of a new, alternatively spliced exon, which we have designated f (for fetal), whose developmentally regulated splicing appears to be a common feature of mammalian skeletal muscle development.

Alternative Splicing↗

PubMed1994

Identification of four genes coding for isoforms of murinoglobulin, the monomeric mouse alpha 2-macroglobulin: characterization of the exons coding for the bait region.

Murinoglobulins are the single chain members of the alpha 2-macroglobulin family of proteinase inhibitors in the mouse. DNA clones representing the genes coding for four different murinoglobulins were isolated from three independent mouse genomic DNA libraries. Sequence analysis demonstrated that in each gene two exons are coding for the bait region. This is the specific protein sequence in each alpha-macroglobulin, which is functionally important since it is extremely sensitive to cleavage by different proteinases. The molecular data established the existence of at least four different murinoglobulin genes. Three of these corresponded to the three cDNA clones previously identified. Sequencing of intron-exon boundaries and intron sizing allowed us to construct physical maps of the region from exon 15 to exon 25 (numbered in comparison to mouse alpha 2-macroglobulin) in each murinoglobulin gene. Southern blotting of genomic DNA from five different mouse strains confirmed this analysis and even suggested the possible existence of a fifth murinoglobulin gene. These data indicate that the mouse presents a genetic repertoire of the alpha 2-macroglobulin family much more complex than originally anticipated. The bait region exon sequences showed a considerably higher degree of divergence (72 to 88% sequence identity) than that of the flanking exon sequences coding for adjacent, structural domains of the murinoglobulin proteinase inhibitors (91 to 96%). Even more surprising was that adjacent intron sequences are conserved as faithfully as the nonbait region coding exons (90 to 96%). These data demonstrate a unique property of the bait region coding sequences, as they apparently are allowed to mutate considerably. This divergency must then confer divergent proteinase inhibitory properties to the resulting proteins.

3T3 Cells↗

PubMed1996

The identification of exons from the MED/PSACH region of human chromosome 19.

We have used exon amplification to identify putative transcribed sequences from an 823-kb contig consisting of 28 cosmids that form a minimum tiling path from the interval 19p12-p13.1. This region contains the genes responsible for multiple epiphyseal dysplasia (MED) and pseudoachondroplasia (PSACH). We have trapped 66 exons (an average of 2.4 exons per cosmid) from pools of 2 or 3 cosmids. The majority of exons (51.5%) show only weak similarity or no similarity (36.3%) to sequences in current databases. Six of 8 exons examined from these groups, however, show cross-species sequence conservation, indicating that many of them probably represent authentic exons. Eight exons show identity or significant similarity to ESTs or known genes, including the human TNF receptor 3 '-flanking region gene, human epoxide hydrolase (EPHX), human growth/differentiation factor (GOF-1), human myocyte-specific enhancer factor 2, the rat neurocan gene, and the human cartilage oligomeric matrix protein gene (COMP). Mutations in this latter gene have recently been shown to be responsible for MED and PSACH.

Amino Acid Sequence↗

PubMed1997

Plectin transcript diversity: identification and tissue distribution of variants with distinct first coding exons and rodless isoforms.

Plectin is a widely expressed protein that is very large in size and that has all the attributes of a multifunctional crosslinking and organizing element of the cytoskeleton. It displays a multidomain structure, versatile binding activities, and subcellular localizations that enable it to strengthen cells against mechanical stress forces. Moreover, hereditary gene defects in plectin cause epidermolysis bullosa simplex (EBS)-MD, a severe skin blistering disease with muscular dystrophy. Here we report the analysis of the exonintron organization of the rat plectin gene and the identification of several different isoforms on the transcriptional level. We show that of 35 coding exons identified, 4 serve as alternative first exons splicing into the same successive exon 2, which is the first of 7 exons encoding a highly conserved actin-binding domain. RNase protection mapping of transcripts containing 3 of the identified 4 alternate first exons revealed their coexpression in rat glioma C6 cells and in a series of different rat tissues that we examined. Significant variations in expression levels of first exons indicated the possibility of tissue-specific promoter usage. In addition, plectin splice variants lacking exon 31 (> 3 kb), which encodes the entire rod domain of the molecule, were identified in a variety of rat tissues. This study provides first insights into a complex plectin gene regulatory machinery with similarities to that of dystrophin.

Alternative Splicing↗

PubMed1998

Complete exon-intron structure of the retina-specific ATP binding transporter gene (ABCR) allows the identification of novel mutations underlying Stargardt disease.

Stargardt disease, an autosomal recessive macular dystrophy of childhood, leading to severe visual impairment, is caused by mutations in the retina-specific ATP binding transporter gene (ABCR). Previously, the ABCR cDNA and part of the exon-intron structure were described. We have determined the complete ABCR exon-intron structure by exon-exon PCR. The ABCR gene encompasses 50 exons, 29 of which are first described here with their corresponding intron-exon boundaries. The discovery of a splicing mutation (571: 2A-->G) and missense mutations in the newly identified exons (R18W, R212C) gives additional support to the broad allelic heterogeneity of Stargardt disease.

ATP-Binding Cassette Transporters↗

PubMed2001

Structure of the human zinc finger protein HIVEP3: molecular cloning, expression, exon-intron structure, and comparison with paralogous genes HIVEP1 and HIVEP2.

Here we report the cloning and characterization of HIVEP3, the newest member in the human immunodeficiency virus type 1 enhancer-binding protein family that encodes large zinc finger proteins and regulates transcription via the kappaB enhancer motif. The largest open reading frame of HIVEP3 contains 2406 aa. and is approximately 80% identical to the mouse counterpart. The HIVEP3 gene is located in the chromosomal region 1p34 and is at least 300 kb with 10 exons. RNA studies show that multiple HIVEP3 transcripts are differentially expressed and regulated. Additionally, transcription termination occurs in the ultimate exon, exon 10, or in exon 6. Therefore, HIVEP3 may produce protein isoforms that contain or exclude the carboxyl DNA binding domain and the leucine zipper by alternative RNA splicing and differential polyadenylation. Sequence homologous to HIVEP3 exon 6 is not found in mouse nor are the paralogous genes HIVEP1 and HIVEP2. Zoo-blot analysis suggests that sequences homologous to the human exon 6 are present only in primates and cow. Therefore, a foreign DNA harboring a termination exon likely was inserted into the HIVEP3 locus relatively recently in evolution, resulting in the acquisition of novel gene regulatory mechanisms as well as the generation of structural and functional diversity.

Amino Acid Sequence↗

PubMed1993

The conserved terminal guanosine of a group I intron can help prevent reopening of the ligated exons.

The highly conserved terminal guanosine of the Tetrahymena group I intron was mutated to an adenosine. The intron still excised itself but more slowly than the wild-type. At very low concentrations of GTP only ligated exons were produced, but at high concentrations of GTP unligated exons accumulated and the 3' exon acquired a GTP at its 5' end. A series of experiments suggested that GTP was primarily reopening the ligated exons, rather than directly cleaving the 3' splice site. 5' Truncated forms of the wild-type intron can cleave RNA in trans. Cleavage takes place downstream of sequences similar to the last few bases of the 5' exon. The ligated exons would therefore be a potential substrate. We believe that the intron uses the terminal guanosine to compete with exogenous GTP until the ligated exons have dissociated from their binding site. Other interactions between intron sequences which are known to aid in 3' splice-site recognition may assist in this process.

Animals↗