PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Exons”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 883 records · Page 49Linked to original sources

Hereditary coproporphyria: exon screening by heteroduplex analysis detects three novel mutations in the coproporphyrinogen oxidase gene.

Hereditary coproporphyria is a dominantly inherited disorder of porphyrin metabolism caused by a partial deficiency of coproporphyrinogen oxidase, the sixth enzyme in the heme synthetic pathway. We investigated the molecular basis of hereditary coproporphyria in three unrelated patients, amplifying each exon of the coproporphyrinogen oxidase gene and performing heteroduplex analysis to look for mutations. Unique heteroduplex patterns were noted in exons 2, 3, and 6. Sequencing revealed different mutations in each patient: a G-->A point mutation encoding a glutamic acid to lysine substitution at codon 101 (E101K), a C-->T point mutation encoding a proline to serine substitution at codon 149 (P149S), and a one base-pair insertion in exon 6 (968insT). No other mutations were found on sequencing the remaining exons and their intron-exon junctions. The two point mutations affect amino acids that are conserved in all species studied to date. The one base-pair insertion in exon 6 is the first frameshift mutation to be described in the coproporphyrinogen oxidase gene. This study adds three new mutations to those that have been previously reported, and all have been restricted to single families. These results indicate that hereditary coproporphyria is a genetically heterogeneous disease.

Amino Acid Sequence↗

A novel missense mutation Ile538Val in the fibroblast growth factor receptor 3 in hypochondroplasia. Mutations in brief no. 122. Online.

Hypochondroplasia and achondroplasia are skeletal dysplasias, characterized by autosomal dominant inheritance and disproportionate short stature, which occurs mainly due to growth failure of the extremities. Both dysplasias have been mapped to fibroblast growth factor receptor 3 (FGFR3) gene. For hypochondroplasia, two point mutations, both responsible for the Asn540Lys substitution in the region coding the tyrosine kinase domain have been reported. Here we report an A to G transition at position 1651, predicting an Ile538Val substitution in the FGFR3, in hypochondroplasia. The substitution is found in a swedish family with three affected members. The criteria for hypochondroplasia were disproportionate short stature and radiological evidence of shortened long bones and decrease or absence of normal increase in interpedicular distances of the lumbar column. The mutation was detected by direct sequencing and restriction enzyme Tai I digestion. The base change was not found in the FGFR3 genes of unaffected members of the family nor in seventy-five unrelated unaffected individuals, suggesting that it was not a polymorphism. The Ile538Val substitution is a conservative amino acid change (a hydrophobic amino acid incorporated for another hydrophobic amino acid). Nevertheless, it is located in the stretch of nine amino acids, which is highly conserved among all the human fibroblast growth factor receptors. Considering the location of this substitution and the segregation with the phenotype in this family, we propose that it is a causative mutation of hypochondroplasia. It is difficult to establish whether the Ile538Val substitution is rare in hypochondroplasia patients or whether the individuals, who have a moderate degree of short stature, rarely seek medical help for the short stature and consequently are rarely diagnosed as affected by hypochondroplasia.

Achondroplasia↗

Spectroscopic evidence revealing polyproline II structure in hydrophobic, putatively elastomeric sequences encoded by specific exons of human tropoelastin.

Elastin, the protein responsible for tissue elasticity, is contained in arterial walls, lungs, and skin. Given the cassette like organization of the human tropoelastin gene, giving rise to alternating exons encoding for crosslink domains and elastomeric domains, it is tempting to suggest that polypeptides encoded by different exons could adopt structures independent of the other exons. The results obtained with the polypeptide sequences encoded by exons 3, 7, and 30 of human tropoelastin are described. It is shown that these hydrophobic exons may partly assume the polyproline II (PPII) structure, as found by circular dichroism studies in aqueous solution. Classical Raman spectroscopy evidences a specific sharp band at 1314 cm(-1), which is assigned to the PPII structure adopted by these exons in the solid state. As these sequences are among those putatively responsible for elastomeric properties, these findings are of particular interest in relation to the current models of the elasticity of elastin.

Amino Acid Sequence↗

Dissection of human tropoelastin: solution structure, dynamics and self-assembly of the exon 5 peptide.

The elastic properties of elastin have essentially been discussed in terms of dominant entropic components, with questions still remaining about whether the basic mechanism is compatible with the classical theory of rubber elasticity. A better understanding of the structure-function relationships in terms of the protein's elastic properties remains an important goal in elastin science. Recently, we succeeded in the exon-by-exon synthesis of all polypeptide sequences encoded by the so-called hydrophobic exons and almost all of the cross-linking exons of human tropoelastin. Among these, the peptide encoded by exon 5 (PGGLAGAGLGA) has been extensively studied by classical spectroscopic methods, such as CD and NMR spectroscopy, and by molecular dynamics simulations. The results obtained clearly evidenced a large flexibility of the polypeptide chain, which oscillates between rather extended conformations, such as PPII, and folded ones, such as beta turns. At the supramolecular level, we obtained evidence by TEM that shows that the peptide encoded by exon 5 is able to self-assemble in fibrillar structures, a result indicating that the "information" for self-assembly is also contained within a small domain of tropoelastin.

Amino Acid Sequence↗

Functional significance of a deep intronic mutation in the ATM gene and evidence for an alternative exon 28a.

Screening for ATM mutations is usually performed using genomic DNA as a template for PCR amplification across exonic regions, with the consequence that deep intronic sequences are not analyzed. Here we report a novel pseudoexon-retaining deep intronic mutation (IVS28-159A>G; g.75117A>G based on GenBank U82828.1) in a patient with ataxia-telangiectasia (A-T), as well as the identification of a previously unrecognized alternative exon in the ATM gene (exon 28a) expressed in lymphoblastoid cell lines (LCL) derived from normal individuals. cDNA analysis using the A-T patient's LCL showed the retention of two aberrant intronic segments of 112 and 190 nt between exons 28 and 29. Minigenes were constructed to determine the functional significance of two genomic changes in the region of aberrant splicing: IVS28-193C>T (g.75083C>T) and IVS28-159A>G, revealing that: 1) the first is a polymorphism; 2) IVS28-159A>G weakens the 5' splice site of the alternative exon 28a and activates a cryptic 5' splice site (ss) 83 nt downstream; and 3) wild-type constructs also retain a 29-nt segment (exon 28a) as part of both the 112- and 190-nt segments. Maximum entropy estimates of ss strengths corroborate the cDNA and minigene findings. Such mutations may prove relevant in planning therapy that targets specific splicing aberrations.

Alternative Splicing↗

A conserved upstream element is essential for transcription of the Leishmania tarentolae mini-exon gene.

We demonstrate that the mini-exon genes of Leishmania tarentolae are individually transcribed by an enzyme pharmacologically identified as RNA polymerase II. To study transcription in these ancient eukaryotes, a stable transformation assay using an episomal mini-exon gene was developed. The introduced mini-exon gene, which had been marked with a 40 bp tag, yielded the predicted tagged transcript. An upstream cis-acting element that was essential for transcription of the mini-exon gene was identified by site-directed mutagenesis. Block substitution mutagenesis of the -1 to +9 and +10 to +19 regions of the exon results in 20- to 100-fold decreased levels of the tagged transcript in steady-state RNA. However, since these two mutations resulted in only a 2- to 3-fold decrease in nascent RNA levels, steady-state levels appear to be affected greatest by the stability of the resulting transcript. In contrast, mutation of the -67/-58 region resulted in undetectable levels of both steady-state and nascent RNA from the introduced gene. We conclude, therefore, that this upstream element, which is highly conserved in all Leishmania species, is a component of the mini-exon gene promoter.

Animals↗

Caspase cleavage of exon 9 deleted presenilin-1 is an early event in apoptosis induced by calcium ionophore A 23187 in SH-SY5Y neuroblastoma cells.

Presenilins (PSs) are mutated in a majority of familial Alzheimer disease (FAD) cases. Mutated PSs may cause FAD by a number of pro-apoptotic mechanisms, or by regulating gamma-secretase activity, a protease involved in beta-amyloid precursor protein processing to the neurotoxic beta-amyloid peptide. Besides their normal endoproteolytic processing, PSs are substrates for caspases, being cleaved to alternative N-terminal and C-terminal fragments. So far little is known about the role of PSs cleavage in the apoptotic machinery. Here, we used SH-SY5Y neuroblastoma cells stably transfected with wild-type or exon 9 deleted presenilin 1 (PS1) in a time-course study after the exposure to the calcium ionophore A23187. During and after exposure to A 23187, intracellular calcium levels were higher in exon 9 deleted PS1 cells as compared with non-transfected and wild-type PS1 transfected cells. Cell death and the enrichment of apoptotic cells after A23187 exposure were increased by overexpression of exon 9 deleted PS1 as compared with the control cell lines. Wild-type PS1 cells were compared with exon 9 deleted PS1 cells and the temporal relationship between PS1 and other caspase substrates cleavages was analyzed. Exon 9 deleted PS1 cells exhibited a higher caspase-3 activation and a greater cleavage of PS1 and poly(ADP-ribose) polymerase (PARP) compared with wild-type PS1 cells. Exon 9 deleted PS1 cleavage occurred earlier than other caspase substrate cleavages (i.e., PARP and gelsolin), simultaneous with minimum detectable caspase-3 activation. Therefore, alternative cleavage of PS1 may play an important role for the regulation of the proteolytic cascade activated during apoptosis.

Apoptosis↗

Differential expression of the four untranslated BDNF exons in the adult mouse brain.

Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophin family of secreted proteins and has important functions in the peripheral and central nervous systems (CNS). Its gene organization is complex, comprising four untranslated exons, each with an associated promoter. We have examined the expression of the four untranslated exons in direct comparison to one another and to the fifth BDNF coding exon by in situ hybridization. Other studies have examined untranslated exon expression in several brain regions in response to specific stimuli; however, this is the first detailed study to describe endogenous exon 1-4 expression throughout the adult mouse brain at baseline conditions. The differential expression of the four untranslated exons seen throughout the brain indicates a complex regulation of BDNF.

Animals↗

ETR-3 represses Tau exons 2/3 inclusion, a splicing event abnormally enhanced in myotonic dystrophy type I.

Altered splicing of transcripts, including the insulin receptor (IR) and the cardiac troponin (cTNT), is a key feature of myotonic dystrophy type I (DM1). CELF and MBNL splicing factor members regulate the splicing of those transcripts. We have previously described an alteration of Tau exon 2 splicing in DM1 brain, resulting in the favored exclusion of exon 2. However, the factors required for alternative splicing of Tau exon 2 remain undetermined. Here we report a decreased expression of CELF family member and MBNL transcripts in DM1 brains as assessed by RT-PCR. By using cellular models with a control- or DM1-like splicing pattern of Tau transcripts, we demonstrate that ETR-3 promotes selectively the exclusion of Tau exon 2. These results together with the analysis of Tau exon 6 and IR exon 11 splicing in brain, muscle, and cell models suggest that DM1 splicing alteration of several transcripts involves various factors.

Alternative Splicing↗

L1 mediated homophilic binding and neurite outgrowth are modulated by alternative splicing of exon 2.

The neural cell adhesion molecule (CAM) L1 is a member of the immunoglobulin superfamily that has been implicated in neuronal adhesion, neurite outgrowth, and axon guidance. The clinical importance of L1 is illustrated by pathological mutations that lead to hydrocephalus, mental retardation, motor defects, and early mortality. The L1 gene is composed of 28 exons, including exons 2 and 27 that are spliced alternatively, and mutations in exon 2 are associated with severe neurological abnormalities in humans. To elucidate the role of L1 exon 2, a recombinant Fc fusion protein called Delta2L1 was constructed lacking the second exon in the extracellular domain of L1. When bound to fluorescent beads, L1 exhibited homophilic binding while Delta2L1 did not. However, L1 beads coaggregated with the Delta2L1 beads. Similarly, in cell binding studies, L1 bound to L1 and Delta2L1 did not bind to Delta2L1 but it bound moderately to L1. Given the reduced binding of Delta2L1, we tested its effect on neurons. By comparison to L1, a lower percentage of dissociated neurons extended neurites on Delta2L1, and there was a modest decrease in the length of the neurites that grew. Neurite outgrowth from reaggregated neurons was much less robust on Delta2L1 than on L1. The combined results indicate that Delta2L1 does not bind homophilically but it can interact with L1 containing exon 2. The reduced binding and neurite promoting activity of Delta2L1 provides an explanation for certain pathological mutations in L1 that lead to clinically apparent disease in the absence of the normal form of L1 in the nervous system.

Alternative Splicing↗

Analysis of the in vitro translation product of a novel-type Drosophila melanogaster aldolase mRNA in which two carboxyl-terminal exons remain unspliced.

Drosophila melanogaster generates three different types of aldolase mRNAs from a single gene by selective usage of the triplicate exons 4 (4 alpha, 4 beta, and 4 gamma), which encode three different isozymes having respective carboxyl termini. We have found the presence of a novel-type mRNA (named alpha beta) in which two final exons, 4 alpha and 4 beta, were retained unspliced. Herein, a cDNA clone containing the alpha beta sequence was inserted into pINIII and expressed in an Escherichia coli system. The product, which exhibited aldolase activity, was found to be isozyme alpha from the primary structure and the enzymological properties, with the 4 alpha sequence alone being present as the carboxyl terminus. In tissues of D. melanogaster, the production of mRNA encoding exon 4 alpha is known to be restrained to a low level. This may be understood by the fact that the aldolase gene of this species does not have a typical poly(A) signal at the 3' end in exon 4 alpha. Instead, the transcript-encoding exons, 4 alpha and 4 beta, might be produced when AATATA, which resides downstream of the coding frame in exon 4 beta, is recognized as a poly(A) signal during RNA processing.

Alternative Splicing↗

Alternative usage of exon 1 of bovine PrP mRNA.

Here we report two types of bovine prion protein (PrP) mRNA that possessed different lengths of the 5'-untranslated region and were expressed in various bovine tissues. The two mRNA species were transcribed from identical positions but differed in the usage of the splice site for exon 1/intron. One mRNA possessed exon 1 consisting of 53 nucleotides and the other possessed exon 1 consisting of 168 nucleotides. Usage of exons 2 and 3 was identical for the two mRNA species. The two mRNA species were detected in all but spleen tissue; the mRNA possessing 168-nt exon 1 was not detected in bovine spleen. This is the first report on the tissue-specific alternative splicing of PrPc mRNA in any other species. Only a low level of PrPc appeared to be present in bovine spleen. These results suggested the possibility that the mRNA possessing 53-nt exon 1 was inefficiently translated into Prp; however, in vitro translation analysis showed no marked difference in translational efficiency between the two mRNA species.

Alternative Splicing↗

An additional exon of stress-inducible heat shock protein 70 gene (HSP70-1).

The HSP70-1 gene, reportedly a single exon, encodes a major stress-inducible 72-kDa heat shock protein (HSP70). We recently demonstrated that patients with major depression had a 162-base pair (bp)-deletion in the 5'-flanking sequence of HSP70-1 mRNA in their peripheral blood mononuclear cells. Present study has been conducted to clarify how this short mRNA is generated, and demonstrated that a novel 385 bp sequence is located 1.1 kb upstream from the HSP70-1 gene of normal subjects. Except for the 162 bp deletion, it is compatible with part of the 5'-flanking sequence of the HSP70-1 gene, and contains another exon of 358 bp (exon 1) that may be connected to the 3'-terminus (exon 3) of the conventional HSP70-1 gene. Alternative transcription of exons 1 and 3 may cause the short mRNA. It is concluded that HSP70-1 gene is constituted of three exons and may cause alternative splicing.

Alternative Splicing↗

Promoter usage for insulin-like growth factor-II in cancerous and benign human breast, prostate, and bladder tissues, and confirmation of a 10th exon.

Upregulation of insulin-like growth factor (IGF)-II expression has been reported for a variety of childhood and adulthood tumors. We determined IGF-II gene promoter usage in human cancerous and benign tissues by semiquantitative RT-PCR using P1-P4-specific primers. Although the human IGF-II gene structure is commonly thought to consist of nine exons and four promoters, we detected substantial utilization of a previously reported exon 4b, which is downstream of exon 4. Thus, exon 4b was intensively studied using 4b-specific primers. IGF-II gene promoter usage is highly variable in malignant and benign breast, prostate, and bladder tissues. While a majority of samples utilized P2-P4 promoters in a variety of combinations, when quantitated, P3 and P4 promoters were much more active than P2 promoter. This study not only demonstrated that IGF-II gene promoter usage is highly variable in malignant and benign tissues, but suggested that alternatively spliced exon 4b should be recognized as a 10th exon.

Adult↗

Peptides encoded by exon 6 of VEGF inhibit endothelial cell biological responses and angiogenesis induced by VEGF.

VEGF induces pathological angiogenesis and is an important target for the development of novel antiangiogenic molecules. In this study, we tested synthetic peptides based on the sequence of VEGF(189) for their ability to inhibit VEGF receptor binding and biological responses. We identified 12-amino acid peptides derived from exon 6 that inhibited VEGF binding to HUVECs, VEGF-stimulated ERK activation, and prostacyclin production. These peptides inhibited VEGF-induced mitogenesis, migration, and VEGF-dependent survival of endothelial cells, but caused no increase in apoptosis in the absence of VEGF. Exon 6-encoded peptides also caused a marked inhibition of VEGF-induced angiogenesis in vitro. Studies of effects of peptides on cross-linking of VEGF to its receptors and on binding of VEGF to porcine aortic endothelial cells expressing either KDR or neuropilin-1 showed that exon 6-encoded peptides effectively blocked the interaction of VEGF with both receptors. Exon 6-derived peptides caused release of bFGF from endothelial cells but inhibited bFGF-dependent ERK activation, cell proliferation and angiogenesis. Our findings indicate that VEGF exon 6-encoded peptides inhibit VEGF-induced angiogenesis, at least in part through inhibition of VEGF binding to KDR. In addition, exon 6-encoded peptides are also effective inhibitors of bFGF-mediated angiogenesis.

Angiogenesis Inhibitors↗

A hereditary C3 deficiency due to aberrant splicing of exon 10.

Hereditary C3 deficiency in a 22-year-old woman was studied. Previous works indicated that C3 could not be detected in the serum of such a patient by enzyme immunoassay. In this study, we demonstrated that C3 genes of this patient and her parents have no gross structural aberration. However, C3 mRNA was almost not detectable in the skin fibroblasts of this patient. The activity of the patient's C3 upstream regulatory elements was tested and showed no functional abnormality. Using reverse-transcriptase polymerase chain reaction (RT-PCR) to amplify RNA from LPS-stimulated patient's fibroblasts, two shorter cDNAs within C3 exon 8 to exon 12 were noted. DNA sequence analysis of the RT-PCR products revealed that one deleted 116 nucleotides of the full exon 10 and the other deleted 34 nucleotides in the 3' region of exon 10. A single base substitution (G to T) in the splice donor site of intron 10 was identified. This aberrant splicing involving exon 10 could result in translational pretermination at exon 11. Thus, this mutation provided the molecular basis for the deficiency of C3 in the patient.

Adult↗

The region encoded by the alternatively spliced exon IIIA in mesenchymal fibronectin appears essential for chondrogenesis at the level of cellular condensation.

Fibronectin in the extracellular matrix of tissues acts as a substrate for cell adhesion and migration during development. Heterogeneity in the structure of fibronectin is largely due to the alternative splicing of at least three exons (IIIB, IIIA, and V) during processing of a single primary transcript. Fibronectin mRNA alternative splicing patterns change from B+A+V+ to B+A-V+ during chondrogenesis. In this report, immunohistochemical analysis demonstrates that while fibronectin protein containing the region encoded by exon IIIB is present throughout the limb at all stages of development, fibronectin protein containing the region encoded by exon IIIA disappears from cartilaginous regions just after condensation in vivo and in high-density mesenchymal micromass cultures in vitro. Treatment of mesenchymal micromass cultures prior to condensation with an antibody specific for the region encoded by exon IIIA disrupts the formation of cellular condensations and inhibits subsequent chondrogenesis in a dose- and time-dependent manner. Furthermore, microinjection of the exon IIIA antibody into embryonic chick limb primordia in vivo results in malformations characterized by smaller limbs and loss of limb skeletal elements. These results strongly suggest that the presence of the region encoded by exon IIIA in mesenchymal fibronectin is necessary for the condensation event that occurs during chondrogenesis.

Alternative Splicing↗

Structural organization of the human type VII collagen gene (COL7A1), composed of more exons than any previously characterized gene.

The human type VII collagen (COL7A1) gene is the locus for mutations in at least some cases of dystrophic epidermolysis bullosa. Here we describe the entire intron/exon organization of COL7A1, which is shown to have 118 exons, more than any previously described gene. Despite this complexity, COL7A1 is compact. Consisting of 31,132 bp from transcription start site to polyadenylation site, it is only about three times the size of type VII collagen mRNA. Thus, COL7A1 introns are small. A 71-nucleotide COL7A1 intron is the smallest intron yet reported in a collagen gene, and only one COL7A1 intron is greater than 1 kb in length. All exons in the COL7A1 triple helix coding region that do not begin with sequences corresponding to imperfections of the triple helix begin with intact codons for Gly residues of Gly-X-Y repeats. This is reminiscent of the structure of fibrillar rather than other nonfibrillar collagen genes. In addition, the COL7A1 triple helix coding region contains many exons of recurring sizes (e.g., 25 exons are 36 bp, 12 exons are 45 bp, 8 exons are 63 bp), suggesting an evolutionary origin distinct from those of other nonfibrillar collagen genes. Sequences from the 5' portion of COL7A1 are presented along with the 3766-bp intergenic sequence, which separates COL7A1 from the upstream gene encoding the core I protein of the cytochrome bc1 complex. The COL7A1 promoter region is found to lack extensive homologies with promoter regions of other genes expressed primarily in skin.

Amino Acid Sequence↗