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At least 217 records · Page 12Linked to original sources

The insulin-binding domain of insulin receptor is encoded by exon 2 and exon 3.

Insulin receptors are disulfide-linked oligotetramers composed of two heterodimers each containing a 130-kDa alpha subunit and a 90-kDa beta subunit. Insulin binds to the extracellular alpha subunit, and in the process stimulates the autophosphorylation of the beta subunit and the expression of tyrosine kinase activity. Studies combining the use of photoaffinity labeling and immunoprecipitation with anti-peptide antibody have directly demonstrated that the cysteine-rich domain, encoded by exon 3, in the alpha subunit is part of the insulin-binding site of the receptor. Experiments with chimeric insulin receptors and chimeric insulin-like growth factor I receptors have confirmed that the cysteine-rich domain constitutes a part of the insulin-binding site. In addition, results from these experiments suggest that the N-terminal sequence, encoded by exon 2, in the alpha subunit also participates in insulin binding. In this review it is proposed that, assuming two insulin-binding sites per each holoreceptor oligotetramer, each insulin-binding domain may contain respectively two sub-domains for hydrophobic and charge contact with insulin, and that high-affinity binding would require the interaction of both subunits with the possibility of each subunit reciprocally contributing one of the sub-domains.

Amino Acid Sequence↗

Acute intermittent porphyria caused by a G to C mutation in exon 12 of the porphobilinogen deaminase gene that results in exon skipping.

Genomic DNA from a patient with acute intermittent porphyria were analyzed by the polymerase chain reaction (PCR)-direct sequencing method. The patient was heterozygote for a point mutation G to C at the last position of exon 12 of the porphobilinogen deaminase (PBG-D) gene. Analysis of the cDNA fragments amplified by PCR revealed that the patient has the abnormal PBG-D mRNA, which does not have exon 12 and exists in an approximately equal amount to the normal mRNA.

Adult↗

Null mutations for exon III and exon IV of the p75 neurotrophin receptor gene enhance sympathetic sprouting in response to elevated levels of nerve growth factor in transgenic mice.

Under normal conditions, expression of the p75 neurotrophin receptor (p75NTR) by sympathetic neurons can increase the affinity of the signaling receptor, trkA, to target-derived nerve growth factor (NGF) at distal axons. We have previously reported that sprouting of sympathetic axons into NGF-rich target tissues is enhanced when p75NTR expression is perturbed, leading to the postulate that p75NTR may restrain sympathetic sprouting in response to elevated NGF levels. These observations were made using mice having a null mutation of the third p75NTR exon, a line that may express a hypomorphic form of this receptor. Since mice carrying a null mutation of the fourth p75NTR exon may not express a similar splice variant, we sought to determine whether these animals possess the same phenotype of enhanced sympathetic sprouting in response to elevated levels of NGF. Both lines of transgenic mice lacking p75NTR displayed similar degrees of sympathetic axonal sprouting into the cerebellum and trigeminal ganglia, two target tissues having elevated levels of NGF protein. Furthermore, the densities of sympathetic axons in both targets were significantly greater than those observed in age-matched NGF transgenic siblings expressing full-length p75NTR. Our new findings provide a comparative analysis of the phenotype in two independent mutations of the same neurotrophin receptor, revealing that p75NTR plays an important role in restricting sympathetic sprouting in response to higher NGF levels.

Animals↗

Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.

Alu exonization, which is an evolutionary pathway that creates primate-specific transcriptomic diversity, is a powerful tool for studying alternative-splicing regulation. Through bioinformatic analyses combined with experimental methodology, we identified the mutational changes needed to create functional 5' splice sites in Alu. We revealed a complex mechanism by which the sequence composition of the 5' splice site and its base pairing with the small nuclear RNA U1 govern alternative splicing. We show that in Alu-derived GC introns the strength of the base pairing between U1 snRNA and the 5' splice site controls the skipping/inclusion ratio of alternative splicing. Based on these findings, we identified 7810 Alus within the human genome that are prone to exonization. Mutations in these Alus may cause genetic disorders or contribute to human-specific protein diversity.

5' Untranslated Regions↗

HLA-B*1559: a hybrid allele including exon 2 of HLA-B35 and exon 3 of HLA-B15 and serologically typed as B35.

The new allele HLA-B*1559 described is of Hispanic origin. This allele carries the exon 2 of HLA-B*35 alleles, and is identical to HLA-B*3501 and the exon 3 of HLA-B*1530. Serologically it is typed as B35. The most likely scenario for its generation seems to be a gene conversion event that involved the, frequent in Hispanic populations, B*1522 allele and a B*1530 allele. A segment of the B*1530 allele that included at least the sequences 412-419 would be transferred on a B*1522 background.

Alleles↗

The R0Har RH:33 phenotype results from substitution of exon 5 of the RHCE gene by the corresponding exon of the RHD gene.

The highly polymorphic Rh (Rhesus) system is encoded by two homologous genes, one encoding the D polypeptide and the other the CcEe polypeptides. Partial D antigens may be caused by gene rearrangements, deletions or point mutations. In this study the molecular basis of R0Har RH:33, a Rh phenotype of low frequency, is described. The R0Har RH:33 phenotype is characterized by partial expression of D, altered expression of e, absence of G and the presence of two antigens of low frequency: Rh33 and FPTT. Southern blot analysis, RHD typing by PCR and sequence analysis of Rh transcripts revealed that the RHD gene is absent in subjects with this phenotype. Apart from the expected RHCE transcripts, a new Rh transcript, RHc(D)(e), was identified in three unrelated individuals expressing R0Har Rh:33. The RHc(D)(e) transcript showed the same sequence as the RHce transcript, with the exception of exon 5, which was substituted by the corresponding exon of the RHD gene. A method for PCR-based genotyping was developed to determine specifically the c(D)(e) haplotype. The c(D)(e) PCR proved to be a reliable alternative method for R0Har RH:33 typing.

Base Sequence↗

ExPrimer: to design primers from exon--exon junctions.

SUMMARY: ExPrimer is a web-based computer program to design primers mainly from a specified exon-exon junction (E-E-jn) of a gene of interest. The tool suggests the optimum primer-pair(s) of which the right (reverse) primer represents a particular E-E-jn of the mRNA. The 'product length' decides the location of the left primer. The results also include all other primer pairs considered and their 'scores'. ExPrimer can use the NCBI BLASTn program for sequence specificity of primers. The tool is useful in many areas of molecular biology research that involve hybridization of short sequences with mRNA or cDNA. AVAILABILITY: http://exprimer.ibab.ac.in/exprimer_html/exprimer.html

Algorithms↗

The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions.

Eukaryotic mRNAs exist in vivo as ribonucleoprotein particles (mRNPs). The protein components of mRNPs have important functions in mRNA metabolism, including effects on subcellular localization, translational efficiency and mRNA half-life. There is accumulating evidence that pre-mRNA splicing can alter mRNP structure and thereby affect downstream mRNA metabolism. Here, we report that the spliceosome stably deposits several proteins on mRNAs, probably as a single complex of approximately 335 kDa. This complex protects 8 nucleotides of mRNA from complete RNase digestion at a conserved position 20-24 nucleotides upstream of exon-exon junctions. Splicing-dependent RNase protection of this region was observed in both HeLa cell nuclear extracts and Xenopus laevis oocyte nuclei. Immunoprecipitations revealed that five components of the complex are the splicing-associated factors SRm160, DEK and RNPS1, the mRNA-associated shuttling protein Y14 and the mRNA export factor REF. Possible functions for this complex in nucleocytoplasmic transport of spliced mRNA, as well as the nonsense-mediated mRNA decay pathway, are discussed.

Animals↗

Dysfunction of the Orleans reeler gene arising from exon skipping due to transposition of a full-length copy of an active L1 sequence into the skipped exon.

We examined the genomic structure of the reeler gene in Orleans reeler mouse mutant. Exon skipping of the reeler gene caused a 220 bp deletion in the transcript, resulting in a frame shift of the reeler gene which disrupts the 8th EGF-like motif of the reeler product. Surprisingly, the skipped exon was inserted by the 7104 bp L1 element which carried the full-length stretch of the mouse L1 sequence, consisting of a 212 bp F-type tandem repeat, open reading frame 1 (ORF1), ORF2, the polyadenylation signal and a poly A stretch. The transposed L1 sequence was flanked by 13 bp of the target sequence at both ends. ORF1 and ORF2 of this L1 repeat element are thought to encode a component of the RNP particle and the reverse transcriptase, respectively. Orleans reeler was originally established by spontaneous mutation caused by L1 insertion, and this L1 sequence is considered to be potentially active for transposition in mouse genome.

Amino Acid Sequence↗

Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.

Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from randomly picked chromosome 21-specific cosmids, to contribute to the creation of the transcription (genic) map of this chromosome and the cloning of its genes. A total of 559 different sequences were identified after elimination of false-positive clones and repetitive elements. Among these, exons for 13 of the 30 known chromosome 21 genes have been "trapped." In addition, a considerable number of trapped sequences showed homologies to genes from other species and to human expressed sequence tags (ESTs). One hundred thirty-three trapped sequences were mapped, and every one mapped back to chromosome 21. We estimate that we have identified portions of up to approximately 40% of all genes on chromosome 21. The genic map of chromosome 21 provides a valuable tool for the elucidation of function of the genes and will enhance our understanding of the pathophysiology of Down syndrome and other disorders of chromosome 21 genes.

Chromosome Mapping↗

Ehlers-Danlos syndrome type IV: a single base substitution of the last nucleotide of exon 34 in COL3A1 leads to exon skipping.

The Ehlers-Danlos syndrome has been classified into nine phenotypic presentations. Type IV is a variant of particular importance because people affected with this genodermatosis are at great risk of spontaneous hemorrhage from vascular rupture or bowel perforation. Recent molecular advances have identified mutations in the gene for type III procollagen as responsible for Ehlers-Danlos syndrome type IV. We report a case of a 14-year-old male with a typical presentation of the type IV variant who was found to have markedly dilated fibroblast cisternae and varying collagen fibril diameter on ultrastructural study. A novel genetic defect was noted by polymerase chain reaction and DNA sequencing of genetic material isolated from skin fibroblast cultures. Analysis of the gene for type III procollagen revealed a single base mutation in the last nucleotide of exon 34. The mutation led to abnormal RNA splicing and skipping of exon 34 on the mRNA level.

Adolescent↗

Molecular basis for hereditary antithrombin III quantitative deficiencies: a stop codon in exon IIIa and a frameshift in exon VI.

Antithrombin III (AT III) is an inhibitor of serine protease (serpin) comprising 432 amino acids. Quantitative AT III deficiencies are associated with a high risk of thrombotic disease. Although this risk is smaller in patients with qualitative AT III deficiencies, the molecular defects characterizing the latter have been the subject of many studies. However, in quantitative AT III deficiencies, only three mutations have been described: Pro 407 to Leu and A1a404 to Thr (both located in the C-terminal part of the AT III molecule) and also a frameshift in exon IIIa. Using the asymmetric polymerase chain reaction (PCR) and genomic DNA analysis by direct sequencing, we detected two mutations in three unrelated families: (i) a C----T transition in exon IIIa in two families, leading to the replacement of the codon corresponding to Arg 129 by a stop codon, and (ii) in the third family, insertion of an adenine in the codon corresponding to Phe 408, a highly conserved serpin amino acid. This insertion altered the reading frame and led to the appearance of a premature stop signal. Patients of all three families were heterozygous for their abnormality. These results show that asymmetric PCR and genomic DNA analysis by direct sequencing permit fast identification of the molecular basis of quantitative AT III deficiencies. It is concluded that in many cases the absence of AT III gene product probably results from point mutation, as previously observed for another serpin, alpha-1-antitrypsin.

Adolescent↗

No evidence for the ascorbic activation site of myrosinase being encoded by end of exon 9, beginning of exon 10.

In summary, we conclude that MA and MB myrosinase genes contain the same set of 12 exons and that data neither support nor exclude the possibility that the portion of the enzyme encoded by exons 9 and 10 contains the ascorbate binding site of the molecule. Indeed, given the fact that both MA and MB myrosinase are activated by ascorbate, it is more reasonable to look for the ascorbate-binding site in areas conserved between the two sequences than in those that have diverged.

Amino Acid Sequence↗

Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1.

In mammalian cells, splice junctions play a dual role in mRNA quality control: They mediate selective nuclear export of mature mRNA and they serve as a mark for mRNA surveillance, which subjects aberrant mRNAs with premature termination codons to nonsense-mediated decay (NMD). Here, we demonstrate that the protein RNPS1, a component of the postsplicing complex that is deposited 5' to exon-exon junctions, interacts with the evolutionarily conserved human Upf complex, a central component of NMD. Significantly, RNPS1 triggers NMD when tethered to the 3' untranslated region of beta-globin mRNA, demonstrating its role as a subunit of the postsplicing complex directly involved in mRNA surveillance.

3' Untranslated Regions↗

Sex-lethal autoregulation requires multiple cis-acting elements upstream and downstream of the male exon and appears to depend largely on controlling the use of the male exon 5' splice site.

The on/off state of the binary switch gene Sex-lethal (Sxl), which controls somatic sexual development in Drosophila melanogaster, is regulated at the level of alternative splicing. In males, in which the gene is off, the default splicing machinery produces nonfunctional mRNAs; in females, in which the gene is on, the autoregulatory activity of the Sxl proteins directs the splicing machinery to produce functional mRNAs. We have used germ line transformation to analyze the mechanism of default and regulated splicing. Our results demonstrate that a blockage mechanism is employed in Sxl autoregulation. However, in contrast to transformer, in which Sxl appears to function by preventing the interaction of splicing factors with the default 3' splice site, a different strategy is used in autoregulation. (i) Multiple cis-acting elements, both upstream and downstream of the male exon, are required. (ii) These cis-acting elements are distant from the splice sites they regulate, suggesting that the Sxl protein cannot function in autoregulation by directly competing with splicing factors for interaction with the regulated splice sites. (iii) The 5' splice site of the male exon appears to be dominant in regulation while the 3' splice site plays a subordinate role.

Animals↗

Expression of exon 3-retaining and exon 3-excluding isoforms of the human growth hormone-receptor is regulated in an interindividual, rather than a tissue-specific, manner.

GH has multiple effects on growth and metabolism, and these functions are mediated through binding to specific cell surface receptors. The human GH receptor (GHR) exists in two known isoforms; in one form exon 3 is present (GHR3+), and in the other, exon 3 is absent (GHR3-). Recent reports have suggested that the expression of the two isoforms is tissue specific and/or developmentally regulated. We used a reverse transcription-polymerase chain reaction assay to study the expression pattern of the two isoforms in a variety of tissues from normal subjects and patients with acromegaly. In skeletal muscle from both normal subjects and patients with acromegaly, the GHR3+ transcript was expressed, either alone or together with the shorter (GHR3-) transcript. When multiple tissues from six subjects were tested, the expression of the two isoforms varied among subjects, whereas different tissues from the same subject showed the same expression pattern. These results indicate that the expression of the GHR isoforms is not tissue specific. Instead, the expression of the GHR isoforms appears to be specific for each individual, suggesting that it is under the control of factors that affect all tissues in the body.

Adipose Tissue↗

Cryptic splice site usage in exon 7 of the human fibrinogen Bbeta-chain gene is regulated by a naturally silent SF2/ASF binding site within this exon.

In this work we report the identification of a strong SF2/ASF binding site within exon 7 of the human fibrinogen Bbeta-chain gene (FGB). Its disruption in the wild-type context has no effect on exon recognition. However, when the mutation IVS7 + 1G>T--initially described in a patient suffering from congenital afibrinogenemia--is present, this SF2/ASF binding site is critical for cryptic 5'ss (splice site) definition. These findings, besides confirming and extending previous results regarding the effect of SF2/ASF on cryptic splice site activation, identify for the first time an enhancer sequence in the FGB gene specific for cryptic splice site usage. Taken together, they suggest the existence of a splicing-regulatory network that is normally silent in the FGB natural splicing environment but which can nonetheless influence splicing decisions when local contexts allow. On a more general note, our conclusions have implications for the evolution of alternative splicing processes and for the development of methods to control aberrant splicing in the context of disease-causing mutations.

Base Sequence↗

Identification of a human CD36 isoform produced by exon skipping. Conservation of exon organization and pre-mRNA splicing patterns with a CD36 gene family member, CLA-1.

During an examination of different cell types for CD36 mRNA splice variants, a partial cDNA from HEL cells was isolated and characterized. This CD36 cDNA had a 309-base pair deletion following the region encoding the first putative transmembrane domain of CD36. The open reading frame of the deleted CD36 cDNA was retained and was predicted to yield a protein lacking 103 amino acid residues. The presence of this variant was confirmed in RNA pools from placental tissue by a reverse transcriptase-coupled polymerase chain reaction assay. Comparison of the HEL CD36 cDNA with the genomic sequence revealed that the mRNA represented by this variant CD36 cDNA was produced by a pre-mRNA splicing reaction that excluded exons 4 and 5. Transient expression of the variant CD36 cDNA in COS-1 cells showed that CD36 immunoreactive protein was expressed on the cell surface but lacked an antigenic epitope defined by amino acid residues 41-143. This cell surface glycoprotein (M(r) approximately 57,000) was of identical molecular weight as a CD36 isoform observed on the surface of HEL cells. The exclusion of exons during CD36 pre-mRNA processing appears to be conserved within one other CD36 gene family member, CLA-1.

Amino Acid Sequence↗