Analysis of donor splice sites in different eukaryotic organisms

Rogozin, Igor B.; Milanesi, Luciano

doi:10.1007/pl00006200

Cited by 146 publications

(103 citation statements)

References 62 publications

(100 reference statements)

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“…Haplotype data suggest that this mutation, like the FGA EX2_EX6 11-kb deletion, is also recurrent, or a very ancient mutation since the c.51011G4T mutation is found on multiple discrete haplotypes. Computer splice prediction analysis [Rogozin and Milanesi, 1997] of the region around the IVS4 donor site detected, in the normal sequence, two distinct donor sites, the physiological one and a second four bases downstream. The c.51011G4T mutation abolishes the normal donor site and in consequence, the c.5101 1G4T mutation was predicted to lead to aberrant usage of the alternative donor site, and a consequent 4-bp frameshift mutation in the majority of transcripts.…”

Section: Splice-site Mutationsmentioning

confidence: 99%

Mutations in the fibrinogen gene cluster accounting for congenital afibrinogenemia: an update and report of 10 novel mutations

Neerman-Arbez

Moerloose

2007

Hum. Mutat.

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Communicated by Arupa GangulyFibrinogen is synthesized in hepatocytes in the form of a hexamer composed of two sets of three polypeptides (Aa, Bb, and c). Each polypeptide is encoded by a distinct gene, FGA, FGB, and FGG, all three clustered in a region of 50 kb on 4q31. Congenital afibrinogenemia is characterized by the complete absence of fibrinogen, the precursor of the major protein constituent of the blood clot, fibrin. Although the disease was first described in 1920, the genetic defect responsible for this disorder long remained unknown. We identified the gene and the first causative mutations for this disease in a nonconsanguineous Swiss family in 1999. Since this first report, 61 additional mutations, the majority in FGA, have been identified in patients with afibrinogenemia (in homozygosity or in compound heterozygosity) or in heterozygosity in hypofibrinogenemia, since many of these patients are in fact asymptomatic carriers of afibrinogenemia mutations. Mutations in the fibrinogen genes may lead to deficiency of fibrinogen by several mechanisms: these can act at the DNA level, at the RNA level by affecting mRNA splicing or stability, or at the protein level by affecting protein synthesis, assembly, or secretion. The expression of selected mutations has shown that mechanisms acting at all three levels play a role in the molecular basis of this disease. We report here the identification of 10 novel mutations, of which eight are localized in FGA, thus increasing the total number of causative mutations identified to 72 and confirming the relative importance of FGA in the molecular basis of fibrinogen deficiency. Hum Mutat 28(6), [540][541][542][543][544][545][546][547][548][549][550][551][552][553] 2007. r r 2007 Wiley-Liss, Inc.

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Section: Splice-site Mutationsmentioning

confidence: 99%

Mutations in the fibrinogen gene cluster accounting for congenital afibrinogenemia: an update and report of 10 novel mutations

Neerman-Arbez

Moerloose

2007

Hum. Mutat.

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“…DNA/protein sequence databases were searched using the BLAST algorithm (Altschul et al, 1990) at the National Center for Biotechnology Information (Bethesda, MD), which was accessed via the World Wide Web. Nucleic acid sequences also were analyzed for the presence of introns with SpliceView (Rogozin and Milanesi, 1997) for the prediction of TATA signals with the HCtata algorithm and for poly(A) signals with the HCpolya algorithm (Milanesi et al, 1996), all of which are available at the WebGene server of the Istituto Tecnologie Biomediche Avanzate (Segrate, Italy). The promoter sequence was dissected using the MatInspector algorithm (Quandt et al, 1995) accessed at the Forshungszentrum für Umwelt und Gesundheit (Neuherberg, Germany).…”

Section: Dna Isolation and Analysismentioning

confidence: 99%

PDE1 Encodes a P-Type ATPase Involved in Appressorium-Mediated Plant Infection by the Rice Blast Fungus Magnaporthe grisea

Balhadère

Talbot

2001

Plant Cell

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Plant infection by the rice blast fungus Magnaporthe grisea is brought about by the action of specialized infection cells called appressoria. These infection cells generate enormous turgor pressure, which is translated into an invasive force that allows a narrow penetration hypha to breach the plant cuticle. The Magnaporthe pde1 mutant was identified previously by restriction enzyme-mediated DNA integration mutagenesis and is impaired in its ability to elaborate penetration hyphae. Here we report that the pde1 mutation is the result of an insertion into the promoter of a P-type ATPase-encoding gene. Targeted gene disruption confirmed the role of PDE1 in penetration hypha development and pathogenicity but highlighted potential differences in PDE1 regulation in different Magnaporthe strains. The predicted PDE1 gene product was most similar to members of the aminophospholipid translocase group of P-type ATPases and was shown to be a functional homolog of the yeast ATPase gene ATC8 . Spatial expression studies showed that PDE1 is expressed in germinating conidia and developing appressoria. These findings implicate the action of aminophospholipid translocases in the development of penetration hyphae and the proliferation of the fungus beyond colonization of the first epidermal cell. INTRODUCTIONOne of the principal reasons why pathogenic fungi are so successful at causing plant disease is their ability to penetrate the plant cuticle directly, often using specialized infection cells called appressoria (Mendgen et al., 1996). A wide variety of fungal pathogens form appressoria, and the development of these cells involves a complex morphogenetic program that results in rapid differentiation of a highly specialized structure (Dean, 1997). The rice blast fungus Magnaporthe grisea is an important pathogen of cultivated rice and has emerged as an experimental model for the study of plant infection processes (for reviews, see Howard and Valent, 1996;Hamer and Talbot, 1998). Magnaporthe develops dome-shaped appressoria, which form at the ends of germ tubes soon after spore germination on the leaf surface. Appressoria attach strongly to the leaf and then generate enormous turgor pressure (up to 8 MPa), which is used to rupture the plant cuticle (Howard et al., 1991). The turgor inside appressoria is generated by a rapid increase in intracellular glycerol levels, which is maintained by a specialized cell wall layer containing melanin (Howard and Ferrari, 1989;de Jong et al., 1997). If melanin biosynthesis is blocked, either by chemical intervention or mutation, then Magnaporthe is unable to penetrate the plant surface and cannot cause disease (Chida and Sisler, 1987;Chumley and Valent, 1990).How such enormous cellular turgor is translated into the substantial invasive force necessary to breach the plant cell wall is not clear, but it appears to involve polarization of the cytoskeleton to the point of infection and localized cell wall modification Howard, 1990, 1992;Bechinger et al., 1999). A narrow penetration hypha forms at t...

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“…The g.4426A>G substitution was particularly interesting as it occurs in the coding region of exon 6 and, as it did not disrupt the reading frame or change codon usage (p.R211R: AGA>AGG), it may have been normally considered as a neutral polymorphism. Therefore, in order to clarify the potential significance of these changes we used several splice-prediction programs based on the search for potential SR binding sequences in the case of ESEfinder (Cartegni et al, 2003), general enhancer sequences in the case of RESCUE-ESE (Fairbrother et al, 2004), or programs such as NNSPLICE (Reese et al, 1997), MaxEntscan and Spliceview (Rogozin and Milanesi, 1997) which evaluate 5' splice site and 3' splice site signal strengths. The results, shown in Table 1, demonstrate that these two mutations do not seem to affect significantly SR protein binding regions (as only minor variations were detected) and that no changes in splicing-affecting sequences could be detected by Rescue-ESE.…”

Section: Resultsmentioning

confidence: 99%

Characterization of two novel GBA mutations causing Gaucher disease that lead to aberrant RNA species by using functional splicing assays

et al. 2005

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The correct identification of disease-causing mutations from the background of harmless nucleotide polymorphisms/substitutions has become a critical issue in the investigation of human genetic diseases. Here, we describe two novel disease-causing splicing mutations in the glucocerebrosidase gene, g.4252C>G and g.4426A>G, that have been found in two patients affected by Gaucher disease. The g.4252C>G substitution occurred in intron 5 and was located 12 nucleotides upstream of exon 6 acceptor site whilst the g.4426A>G mutation was located within this exon, 12 nucleotides upstream of the donor site. An in silico analysis suggested that both mutations could have altered the splicing process of exon 6 by creating a novel acceptor and donor site, respectively. However, because the wild-type acceptor and donor sites of exon 6 were not apparently affected, the severity of both mutations could not be established by simple sequence analysis alone. Nonetheless, the use of minigene functional assays to complement transcript analysis of patient fibroblasts shows that both mutations cause the almost complete switch of splice site usage from the wild-type to the newly-created ones, thus providing a functional explanation for the appearance of disease. © 2005 Wiley-Liss, Inc.KEY WORDS: GBA gene; Gaucher disease; splicing mutations; functional splicing assay INTRODUCTIONConsidering the complexity of the pre-mRNA splicing process (Matlin et al., 2005) it is not surprising that alterations in this pathway have been reported in a great variety of genetic diseases (Caceres and Kornblihtt, 2002;Nissim-Rafinia and Kerem, 2002;Faustino and Cooper, 2003;Garcia-Blanco et al., 2004). Therefore, an increasingly critical issue for eventual diagnosis, therapy, or counselling is represented by the correct identification of which nucleotide changes represent benign polymorphisms and which may result in potential disease-causing mutations (Pagani and Baralle, 2004;Baralle and Baralle, 2005). To facilitate these distinctions, the use of computer assisted prediction methods has become very useful. However, a correct evaluation of their effects can DOI: 10.1002/humu.9391 2 Dominissini et al.be achieved only by the use of functional splicing assays, as described in this report concerning two novel splicing mutations in patients affected by Gaucher disease.Gaucher disease is the most frequent lysosomal storage disorder caused by an autosomal recessive deficiency of acid beta-glucosidase (E.C.3.2.1.45) that in turn leads to the accumulation of glucocerebroside. Based on the presence and progression of primary central nervous system involvement, Gaucher disease has been classified in Type 1 (non-neuronopathic, MIM# 230800), Type 2 (acute neuronopathic, MIM# 230900) and Type 3 (subacute neuronopathic, MIM# 231000) (Beutler and Grabowski, 2001). The glucocerebrosidase gene (GBA; MIM# 606463; GenBank accession no. J03059.1) is located on chromosome 1q21 and contains 11 exons spread out in approximately 7.5 kb of genomic sequence. A highly homologous ∼5.5...

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Analysis of donor splice sites in different eukaryotic organisms

Cited by 146 publications

References 62 publications

Mutations in the fibrinogen gene cluster accounting for congenital afibrinogenemia: an update and report of 10 novel mutations

Mutations in the fibrinogen gene cluster accounting for congenital afibrinogenemia: an update and report of 10 novel mutations

PDE1 Encodes a P-Type ATPase Involved in Appressorium-Mediated Plant Infection by the Rice Blast Fungus Magnaporthe grisea

Characterization of two novel GBA mutations causing Gaucher disease that lead to aberrant RNA species by using functional splicing assays

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