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At least 217 records · Page 12Linked to original sources

PubMed1997

Evolution of shorter and more hydrophilic transthyretin N-termini by stepwise conversion of exon 2 into intron 1 sequences (shifting the 3' splice site of intron 1)

Transthyretin cDNA was cloned from Eastern Grey Kangaroo liver and its nucleotide sequence determined. Analysis of the derived amino acid sequence of kangaroo transthyretin, together with data obtained previously for transthyretins from other vertebrate species [Duan, W., Richardson, S. J., Babon, J. J., Heyes, R. J., Southwell, B. R., Harms, P. J., Wettenhall, R. E. H., Dziegielewska, K. M., Selwood, L., Bradley, A. J., Brack, C. M. & Schreiber, G. (1995) Eur. J. Biochem. 227, 396-406], showed that the N-terminus is the region which changes most distinctly during evolution. It has been shown for human, mouse and rat transthyretins, that this region is encoded by DNA at the border of exon 1 and exon 2. Therefore, this section of transthyretin genomic DNA was amplified by PCR and directly sequenced for the Buffalo Rat, Tammar Wallaby, Eastern Grey Kangaroo, Stripe-faced Dunnart, Short-tailed Grey Opossum and White Leghorn Chicken. The splice sites at both ends of intron 1 were identified by comparison with the cDNA sequences. The obtained data suggest that the N-termini of transthyretin evolved by successive shifts of the 3' splice site of intron 1 in the 3' direction, resulting in successive shortening of the 5' end of exon 2. At the protein level, this resulted in a shorter and more hydrophilic N-terminal region of transthyretin. Successive shifts in splice sites may be an evolutionary mechanism of general importance, since they can lead to stepwise changes in the properties of proteins. This could be a molecular mechanism for positive Darwinian selection.

Amino Acid Sequence↗

PubMed2003

Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure.

Gene duplication is considered to be a source of genetic information for the creation of new functions. The Arabidopsis thaliana genome sequence revealed that a majority of plant genes belong to gene families. Regarding the problem of genes involved in the genesis of novel organs or functions during evolution, the reconstitution of the evolutionary history of gene families is of critical importance. A comparison of the intron/exon gene structure may provide clues for the understanding of the evolutionary mechanisms underlying the genesis of gene families. An extensive study of A. thaliana genome showed that families of duplicated genes may be organized according to the number and/or density of intron and the diversity in gene structure. In this paper, we propose a genomic classification of several A. thaliana gene families based on introns in an evolutionary perspective.

Arabidopsis↗

PubMed1990

Phosphorylation-dependent binding of a 138-kDa myc intron factor to a regulatory element in the first intron of the c-myc gene.

A 138-kDa nuclear protein was identified from HeLa cell extracts as a factor which binds to a previously described 20-base pair cis element located in the intron I of the c-myc gene. This myc intron factor (MIF) binds to the wild type c-myc sequence but does not bind under similar conditions to c-myc from Burkitt's lymphoma which contain point mutations in this binding region. We have demonstrated that the 138-kDa MIF is a phosphoprotein and that treatment of the purified MIF with potato acid phosphatase abolished binding to its 20-base pair c-myc recognition sequence; binding activity was protected by inclusion of phosphatase inhibitors. These results suggest that phosphorylation is required for the specific DNA-MIF interaction in vitro and that the phosphorylation state of MIF may be an important factor in controlling c-myc expression in vivo.

Acid Phosphatase↗

PubMed2001

Clonal maintenance of imprinted expression of SNRPN and IPW in normal lymphocytes: correlation with allele-specific methylation of SNRPN intron 1 but not intron 7.

DNA methylation is a heritable and reversible modification to CpG sites in the mammalian genome. Parental allele-specific methylation is hypothesized to be important in the establishment and maintenance of imprinted gene expression; however, dynamic changes in allele-specific patterns have been observed. The upstream regulatory region of the small nuclear riboprotein N gene (SNRPN) is an important imprinting control region (ICR) for establishing and maintaining the methylation imprint in the locus on 15q11-13 associated with Prader-Willi and Angelman syndromes (PWS). To compare directly the role of allele-specific methylation patterns and the maintenance of imprinted expression in the PWS region, clonal populations of normal T lymphocytes were cultured for 22-25 generations. A novel long-range semi-nested polymerase chain reaction (PCR) strategy was utilized in order to span two different methylation sites, and a polymorphism within SNRPN was used so that allele-specific methylation of both sites could be determined. Reverse transcription/PCR followed by polymorphism analysis was also performed in order to determine parental allele-specific transcription. Exclusive paternal expression at both SNRPN and IPW was maintained in all T cell clones and correlated with maternal methylation of the intron 1 NotI site. In contrast, biallelic methylation was observed in all clones at the previously described paternally methylated HpaII site in intron 7. These results demonstrate that the maintenance of paternal expression of SNRPN and IPW correlates with a strict clonal maintenance of allele-specific methylation at the CpG-dense 5' end of SNRPN. Differential maintenance of methylation sites within imprinted genes may depend on the density and chromatin organization of surrounding CpG sites.

Alleles↗

PubMed1980

Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron.

We have determined the DNA sequence of the wild type and mutated introns as well as their flanking exons in the yeast mitochondrial gene specifying cytochrome b. The second intron (box3) encodes a trans-acting protein "mRNA maturase" responsible for splicing and maturation of cytochrome b mRNA. This protein is interlaced with cytochrome b exon sequences. Its biosynthesis is subject to a negative feedback which may constitute a regulatory mechanism for the expression of split genes.

Base Sequence↗

PubMed1983

Two intron sequences in yeast mitochondrial COX1 gene: homology among URF-containing introns and strain-dependent variation in flanking exons.

The DNA sequences of two optional introns in the gene for subunit I of cytochome c oxidase in yeast mitochondrial DNA have been determined. Both contain long unassigned reading frames (URFs). These display regions of amino acid homology with six other URFs, two of which encode proteins involved in mitochondrial RNA splicing. Such conserved regions may thus define functionally important domains of proteins involved in RNA processing. This homology also implies that these URFs had a common ancestral sequence, which has been duplicated and dispersed around the genome. Comparison of the flanking exons in the long strain KL14-4A with their unsplit counterpart in D273-10B reveals clustered sequence differences, which lead in D273-10B to codons rarely used in exons. These differences may be linked to the loss or absence of one of the optional introns.

Base Sequence↗

PubMed2006

Functional splicing assay shows a pathogenic intronic mutation in neurofibromatosis type 1 (NF1) due to intronic sequence exonization.

Genomic variations with no apparent effect ("neutral polymorphisms") may have a significant effect on splicing. The effect of this type of mutation is difficult to spot, unless a functional assay is undertaken. In our study, DNA sequencing of a patient with clinically defined neurofibromatosis type 1 (NF1) showed only a single polymorphism in intron 30 due to an A>G transition 279 nucleotides from the 3' splice site. Using a minigene splicing assay we conclusively show that this change produces a cryptic exon with a 3' SS defined by the nucleotide change and the unexpected activation of a very weak 5'SS. Further site directed mutagenesis studies aimed at identifying the signals involved in the cryptic exon inclusion were carried out. Interestingly we find that particular characteristics of the cryptic 5' SS are essential for its inclusion. Significantly an additional single nucleotide change disrupting the cryptic 5'ss consensus sequence rescues the effect of the pathogenetic mutation resulting in normal splicing.

Base Sequence↗

PubMed1989

Cytochrome oxidase subunit II sequences in Petunia mitochondria: two intron-containing genes and an intron-less pseudogene associated with cytoplasmic male sterility.

The mitochondrial genome of Petunia hybrida contains two transcribed cytochrome oxidase subunit II (coxII) genes. The coding region of both genes is split by a 1.3 kb group II intron. Unlike coxII-1, which is similar to other sequenced plant coxII genes, the coxII-2 coding region is extended by 48 codons. The cytoplasmic male sterile (CMS) Petunia contains one coxII gene similar in structure and transcript pattern to the coxII-1 gene found in the fertile genome. Comparison of the sequenced coxII genes from the fertile mitochondrial genome with the coxII sequences present in the CMS-associated pcf gene from the CMS genome (Young and Hanson 1987) suggests that pcf is a processed pseudogene. A model for the generation of pcf is presented.

Amino Acid Sequence↗

PubMed2006

A splice-supporting intronic mutation in the last bp position of a cryptic exon within intron 6 of the CYBB gene induces its incorporation into the mRNA causing chronic granulomatous disease (CGD).

Chronic granulomatous disease (CGD) is caused by a defect in both the host's defenses and its regulation of inflammation normally provided by phagocytes and other leukocytes. As in the case described here, it is not uncommon that CGD patients are diagnosed late, only after organ-damaging manifestations have already progressed. In this patient, we found that CGD arose due to a splice-supporting mutation in the last position of a cryptic exon towards the middle of intron 6 of the CYBB (gp91-phox) gene. The mutation led to the insertion of 56 bp into most of the CYBB mRNA of leukocytes causing a frame shift and a premature stop codon. The normal cryptic exon was also found to be mildly active in some tissues other than leukocytes in healthy donors, to be conserved in many primates, and to a lesser degree in other mammals. Some sequence similarity suggests that the cryptic exon may have originated from a mammalian interspersed repetitive (MIR) element. Taken together, we clarify an unusual disease-causing mutation, indicate its evolutionary background and emphasize the importance of a timely diagnosis of CGD.

Base Sequence↗

PubMed1994

Intron mobility. Invasive introns.

The evidence that introns in fungal and plant organellar DNAs are mobile genetic elements has strengthened significantly; like Shaw's cockney heroine, Eliza Doolittle, they cannot help but betray their origins.

DNA, Fungal↗

PubMed1996

A semi-automated method for analysis of intron 13 and intron 22 dinucleotide repeat polymorphisms of the factor VIII gene.

A semi-automated method has been developed for the simultaneous analysis of two micro-satellite repeat polymorphisms located in intron 13 and 22 of the Factor VIII gene. The fluorescent dyes, 6-FAM-and HEX-phosphoramidites were used to 5'-end label the respective 5' primers of these two microsatellite repeats and a multiplex polymerase chain reaction (PCR) devised for amplification. The PCR product was loaded onto the gel with DNA size marker labelled with ROX. A total of 24 samples could be analysed simultaneously on an automated DNA sequencer. The results were computed using a dedicated software, with assignment of PCR product size in basepair. This method compares well with the conventional manual procedure using radio-labelled primers, but at the same time overcomes many of the inherent disadvantages associated with the latter method.

Alleles↗

PubMed2004

A ternary complex of transcription factors, Nishéd and NFATc4, and co-activator p300 bound to an intronic sequence, intronic regulatory element, is pivotal for the up-regulation of myosin light chain-2v gene in cardiac hypertrophy.

Transcriptional up-regulation of the myosin light chain-2 (MLC-2v) gene is an established marker for hypertrophic response in cardiomyocytes. Despite the documentation on the role of several cis-elements in the MLC-2v gene and their cognate proteins in transcription, the mechanism that dictates the preferential increase in MLC-2v gene expression during myocardial hypertrophy has not been delineated. Here we describe the properties of a cardiac specific intronic activator element (IRE) that shares sequence homology with the repressor element, the cardiac specific sequence, in the chicken MLC-2v gene. The transcription factor, Nishéd, that recognizes both IRE and the cardiac specific sequence potentiates the transcription of the MLC-2v gene via interaction with another transcription factor, nuclear factor of activated T cells, and the co-activator p300 at the IRE site. Angiotensin II (Ang II), a potent agonist of hypertrophy, causes induction of the MLC-2v gene transcription, which correlates well with the enhanced binding of Nishéd-nuclear factor of the activated T cells-p300 complex to IRE in the gel mobility shift assay. Losartan, an antagonist of Ang II receptor (AT1), abolishes the agonist-dependent stimulation of IRE/protein interaction and the consequent increase in MLC-2v gene transcription. These results together have thus established a transcriptional role of IRE as a direct target sequence of Ang II-mediated signaling that appears to be pivotal in the mechanism underlying the up-regulation of the MLC-2v gene during cardiac hypertrophy.

Amino Acid Sequence↗

PubMed1996

[Hemophilia A: analysis of intron 18 and intron 7 of factor VIII gene and their role in a diagnostic strategy for carrier detection in a Chilean population].

Hemophilia A is an X-linked disorder of coagulation caused by a deficiency of factor VIII. A larger number of different mutations in the VIII gene have been identified. Thus, the detection of female carriers, depends upon the analysis of DNA polymorphisms in and near the factor VIII gene. Our aim was to develop a strategy, earlier reported, for carrier testing in families at risk of hemophilia A. In this study, we analyzed the DNA polymorphisms in 26 affected families, with use of the factor VIII intragenic polymorphisms identified by the restriction enzymes BclI and AlwNI, and by differential hybridization with sequence-specific oligonucleotide probes recognizing BclI and AlwNI polymorphism. While the DNA polymorphism detected by BcilI site in intron 18 of the factor VIII gene was informative for 38% families studied, the AlwNI/intron 7 polymorphism provided additional information (4%). The carrier status of the remaining 58% could be determined utilizing the other polymorphisms suggested by strategy. The two polymorphic sites used combined with the other polymorphisms, intragenic and extragenic, can generate levels of informativeness greater than 98%. We concluded that the strategy for carrier testing would be a good alternative in genetic counselling for hemophilia A, but its limitations must be carefully taken into account.

Chile↗

PubMed2001