PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Alternative Splicing”

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 1,621 records · Page 90Linked to original sources
PubMed1988

cDNA cloning of porcine transforming growth factor-beta 1 mRNAs. Evidence for alternate splicing and polyadenylation.

Most eukaryotic cells encode principally a 2.5-kilobase (kb) transforming growth factor (TGF)-beta 1 mRNA. However, we have found two major TGF-beta 1 RNA species, 3.5 and 2.5 kb long, in porcine tissues. The 3.5-kb species has a longer 3'-untranslated sequence generated by the selection of an alternate polyadenylation site. There is a 117-nucleotide sequence within this unique 3' region, which is similar to the PRE-1 repetitive sequence of unknown function, reported earlier in the porcine genome. We have also cloned and characterized an alternately spliced mRNA species specific for the TGF-beta 1 gene, in which exons IV and V of the corresponding human TGF-beta 1 gene are deleted. The nucleotide sequence of this cDNA clone predicts a putative precursor protein of 256 amino acids; the N-terminal 211 amino acids of this putative protein are identical to the TGF-beta 1 precursor protein (exons I, II, and III of the human TGF-beta 1 gene), but the C-terminal 45 amino acids are distinct, due to a frameshift in the translation of exons VI and VII. In addition we provide data for the existence of other mRNA species generated in a tissue-specific manner either by alternate splicing or by heterogeneous 5' leader sequences.

Amino Acid Sequence↗
PubMed1993

An alternatively spliced variant of mRNA for the human receptor for urokinase plasminogen activator.

Using 3' RACE (rapid amplification of cDNA ends), we have isolated a cDNA variant for the receptor for human urokinase plasminogen activator (uPAR). The deduced protein includes the amino-terminal ligand binding domain in uPAR, but lacks the carboxy-terminal membrane attachment by a glycolipid anchor. Genomic DNA analysis showed that the uPAR mRNA variant is generated by alternative splicing. The new variant mRNA is expressed in various human cell lines and tissues and both variants are up-regulated by phorbol ester in A549 cells. We propose that the alternatively spliced uPAR mRNA encodes a soluble uPA binding protein, the possible function of which is discussed.

Amino Acid Sequence↗
PubMed1999

Cloning of the murine unconventional myosin gene Myo9b and identification of alternative splicing.

We report the cloning of a cDNA for the mouse unconventional myosin Myo9b, the orthologue of the rat myr5 and human MYOIXb genes. A full-length spleen cDNA of 7087bp encoding a protein of 1961 amino acids was isolated. By RT-PCR, we show that Myo9b is expressed in a wide range of tissues, including heart, brain, muscle and inner ear. In addition, we have identified two alternatively spliced exons. Equivalent exons have not been previously reported for either the human or rat homologues. These exons are located in the Myo9b specific actin-binding site insert of the head domain and in the tail region. A third splice form utilizing an alternative reading frame within the 3'UTR is also described. Several polymorphisms within the coding region were identified; of interest is an in-frame 33bp imperfect duplication within the tail region that was observed only in the C57Bl/6 strain. Myo9b has been previously mapped to mouse chromosome 8 and is a candidate for the mouse mutations myodystrophy and quinky.

3' Untranslated Regions↗
PubMedDate not supplied

Alternative splicing of the K-ras gene in mouse tissues and cell lines.

The mRNA from the K-ras protooncogene is alternatively spliced into 2 transcripts, K-ras4A and K-ras4B, which possess 2 alternative fourth coding exons. In the present study, expression of K-ras4A and K-ras4B transcripts in 8 organs, including heart, brain, spleen, lung, liver, skeletal muscle, kidney, and testis, from BALB/c mice were determined by Northern blot hybridization. K-ras4B, observed in all organs, accounted for approximately 90% to 99% of total K-ras mRNA. K-ras4A was detected only in lung, liver, and kidney. In addition, K-ras expression in lungs and K-ras4A/K-ras4B ratios in lung, liver, spleen, and kidney from A/J, BALB/c, C3H/HeJ, and C57BL/6J mice were determined. A/J lungs expressed K-ras mRNA 2-fold higher than C3H/HeJ or C57BL/6J lungs, whereas K-ras mRNA expression in BALB/c lungs was intermediate. Higher percentages of K-ras4A mRNA were found in lungs and kidneys from A/J and BALB/c mice, as compared with those from C3H/HeJ and C57BL/6J mice. Levels of K-ras4A and K-ras4B mRNAs were also examined in 20 NIH 3T3 cell lines transformed by DNA from spontaneous A/J mouse lung tumors. K-ras4A was expressed 2- to 3-fold higher in these cell lines than in nontransformed NIH 3T3 cells and in C10 cell lines. These results suggest that: (1) there may be functional differences between the protein encoded by K-ras4A and that encoded by K-ras4B in each tissue type, and in tumor cells; and (2) K-ras mRNA expression and K-ras4A/K-ras4B ratios detected in lung tissues from different strains of mice correlate with susceptibility to tumor induction.

3T3 Cells↗
PubMed2006

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.

MOTIVATION: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and mechanisms of these phenomena. RESULTS: We have developed an algorithm that classifies all observed units of ASTI into an extendable set of distinct types (e.g. cassette type) by converting a collection of alignments between a genomic DNA sequence and cDNA sequences into binary description. This description system can uniquely and compactly encode not only typical patterns but also any rare patterns that are usually collectively assigned to 'others.' More than 150 distinct ASTI types were found when this system was applied to genome-wide detection of ASTI units in human and five other eukaryotes. AVAILABILITY: The data detected by this system are available through ASTRA (http://alterna.cbrc.jp/), a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand.

Algorithms↗
PubMed1994

Alternative splice form of type II procollagen mRNA (IIA) is predominant in skeletal precursors and non-cartilaginous tissues during early mouse development.

Type II collagen, generally considered to be characteristic of cartilage, has been localized in specific non-cartilaginous structures during embryogenesis and development of the skeleton. Type II procollagen is synthesized in two different forms generated by alternative splicing of exon 2 in the precursor mRNA transcript. One form (type IIA procollagen) contains a large cysteine-rich domain in the NH2-terminal propeptide, while the second form (type IIB procollagen) does not. These two forms are spatially expressed during development and chondrogenesis with the type IIB procollagen mRNA primarily expressed by chondrocytes while the IIA form is expressed in chondroprogenitor cells (Sandell et al. [1991] J. Cell Biol. 114:1307-1319). The present study demonstrates that the early non-cartilage expression, by somites, mesenchymal and epithelial cells, is predominantly the alternate splice form, type IIA procollagen mRNA. Later in development, the type IIB mRNA splice form is expressed by chondrocytes. During the development of intramembranous bones, such as the mandible, type IIA procollagen mRNA is also expressed. In this tissue, the splice form does not switch to type IIB mRNA and no cartilage is formed. These results show that expression of type IIA mRNA, whether by epithelial or mesenchymal cells, precedes formation of overt skeletal structures.

Animals↗
PubMed1992

Two types of murine CD34 mRNA generated by alternative splicing.

To characterize and clarify the function of CD34 antigen experimentally, we isolated two types of CD34 mRNA from a cDNA library of murine stromal cell line, PA-6 stimulated with lipopolysaccharide (LPS) and 12-o-tetra-decanoylphorbol 13-acetate (TPA) using a human CD34 probe. In addition to the clone (open reading frame [ORF]:1149bp) reported by Brown et al, a novel clone (ORF:978 bp) was obtained. The difference between the two clones was in the cytoplasmic portion of CD34; the former has 73 amino acids, while the latter has 16. We investigated the genomic sequence of cytoplasmic portion and found conserved nucleotide sequences at the exon-intron junction (GT ... AG). Thus, it was concluded that alternative splicing gave two types of CD34 mRNA. A novel clone contains the longer cDNA, including a insert of 156 bp, but results in a shorter predicted coding sequence because of the introduction of an inframe stop codon. Northern blot analysis using a murine cDNA probe (HindIII fragment, 900 bp) showed that CD34 was highly expressed in the brain and testis, and moderately in the thymus, spleen, and bone marrow, but not in adult liver. However, day 12 to 14 fetal liver cells showed significant expression of CD34. Quantitative reverse transcription polymerase chain reaction showed that spleen, thymus, bone marrow, and testis RNA gave two bands of almost equal intensity, but in the brain a novel clone was expressed three times more than the other clone. Furthermore, Northern blot analysis using a probe (156 bp) specific for the spliced intracellular region confirmed the significant mRNA expression of a novel clone. Although the biologic significance of alternative splicing remains to be elucidated, it is suggested that a different carboxyterminal tail causes a change in signal transduction.

Amino Acid Sequence↗
PubMed1991

Alternate splicing of mRNAs encoding human mast cell growth factor and localization of the gene to chromosome 12q22-q24.

Human mast cell growth factor (MGF) complementary DNAs (cDNAs) were cloned from HeLa cells using the polymerase chain reaction with oligonucleotides corresponding to murine and human MGF sequences. Sequencing of the cloned human MGF polymerase chain reaction products revealed two types of cDNA: a full length form corresponding in size to the murine cDNA, and an alternately spliced clone with a deletion of the sixth exon of the gene. Since membrane-bound MGF is predicted to be proteolytically cleaved within the sequences encoded by exon 6 to generate a soluble protein, this alternately spliced cDNA would likely encode a noncleavable, membrane-bound form of MGF. No difference in biological activity on human bone marrow cells was observed with recombinant, soluble forms of both types of human MGF protein. Our previous localization of the murine MGF gene to the Sl locus on chromosome 10 suggested (via conserved linkage groups) that the human MGF gene would be located on human chromosome 12. Therefore, rodent-human somatic cell hybrids with or without an entire human chromosome 12 and hybrids retaining partial 12 were tested by Southern blot analysis and used to show the presence of the human Mgf locus at chromosome region 12q. Chromosomal in situ hybridization localized the gene to 12q22-q24 in the region predicted by the comparative mapping of the murine Mgf/Sl locus.

Amino Acid Sequence↗
PubMed1991

Differential expression of the alternatively spliced exons of murine CD45 in Th1 and Th2 cell clones.

Antigen-specific murine CD4+ T cell clones can be divided into functionally distinct subsets known as Th1 and Th2. To date these cells have been indistinguishable by surface phenotype. This report identifies two anti-CD45R monoclonal antibodies (14.8 and C363.16A) that bind preferentially to Th2 cells. Further analysis of the CD45-specific mRNA in Th1 and Th2 cells shows clear differences between these two cell types. Th1 cell clones express mRNA for the two smallest forms of CD45 containing none or only one of the alternatively splices exons. In contrast, Th2 cell clones express predominantly the high molecular weight isoforms of CD45 containing two or three of the alternatively spliced exons.

Animals↗
PubMed2005

Structural basis of the interaction between P-element somatic inhibitor and U1-70k essential for the alternative splicing of P-element transposase.

P-element transposition in Drosophila is regulated by tissue-specific alternative splicing of the P-element transposase pre-mRNA. In somatic cells, the P-element somatic inhibitor (PSI) protein binds to exon 3 of the pre-mRNA and recruits U1 small nuclear ribonucleoprotein (snRNP) to the F1 pseudo-splice site. This abrogates binding of U1 snRNP to the genuine 5' splice site, thereby preventing excision of the third intron. Two homologous short sequences, referred to as the A and B boxes, near the C terminus of PSI bind to U1-70k protein within U1 snRNP. We have now mapped the AB box-binding site of U1-70k to a short proline-rich sequence at the C terminus. Our NMR study shows that the B box forms an anti-parallel helical hairpin in which four highly conserved aromatic residues form a cluster on one face of the first helix. This hydrophobic cluster interacts extensively with the proline-rich region of the U1-70k protein.

Alternative Splicing↗
PubMed1994

Tissue-dependent alternative splicing of mRNA for NACP, the precursor of non-A beta component of Alzheimer's disease amyloid.

A cDNA clone encoding an alternatively spliced form of the precursor of the non-A beta component of Alzheimer's disease amyloid (NACP) was isolated from a human fetal brain cDNA library. This cDNA contains the entire NAC coding sequence but lacks an 84-base-pair nucleotide stretch 3' to the NAC sequence, resulting in a 112-amino-acid protein, NACP112, in contrast with the originally cloned molecule, NACP140. RT-PCR analysis demonstrated that the mRNA for two types of NACP mRNA are expressed in both fetal and adult brain. Northern blot analysis revealed that NACP140 mRNA was expressed mostly in brain and in minor amount in all the tissues examined. However, the expression levels of NACP140 mRNA apart from brain were higher in heart, skeletal muscle, and pancreas, contrasting with the predominant expression of total NACP mRNA in brain with a slight expression in placenta. These results suggest differential regulation of NACP RNA splicing among tissues.

Alternative Splicing↗
PubMed2005

TCOF1 mutation database: novel mutation in the alternatively spliced exon 6A and update in mutation nomenclature.

Recently, a novel exon was described in TCOF1 that, although alternatively spliced, is included in the major protein isoform. In addition, most published mutations in this gene do not conform to current mutation nomenclature guidelines. Given these observations, we developed an online database of TCOF1 mutations in which all the reported mutations are renamed according to standard recommendations and in reference to the genomic and novel cDNA reference sequences (www.genoma.ib.usp.br/TCOF1_database). We also report in this work: 1) results of the first screening for large deletions in TCOF1 by Southern blot in patients without mutation detected by direct sequencing; 2) the identification of the first pathogenic mutation in the newly described exon 6A; and 3) statistical analysis of pathogenic mutations and polymorphism distribution throughout the gene.

Alternative Splicing↗
PubMed2003

Subordination stress alters alternative splicing of the Slo gene in tree shrew adrenals.

It was previously hypothesized that stress hormones regulate the alternative splicing of Slo potassium channels, thereby tuning the intrinsic excitability of adrenal chromaffin cells. Male tree shrews subjected to chronic stress by exposure to a dominant male develop robust symptoms with parallels to human depression. We report here that adrenals from males subjected to 4-6 weeks of subordination have a significantly smaller proportion of Slo transcripts with the optional STREX exon (STRess-axis regulated EXon) than unstressed male adrenals. Female adrenals (unstressed) had even lower levels than stressed males. These data suggest both behavioral regulation and sexual dimorphism in ion channel structure. We hypothesize that chromaffin cell excitability and sympathoadrenal function will be altered, and speculate that this may favor passive coping responses in subordinate males and females.

Adrenal Glands↗
PubMed2005

Identification of HLA-A*0111N: a synonymous substitution, introducing an alternative splice site in exon 3, silenced the expression of an HLA-A allele.

A new variant of the HLA-A*010101 allele designated as HLA-A*0111N, previously known as HLA-A*010101var, was identified in a patient requiring a stem-cell transplantation. The patient was typed by serologic methods as HLA-A2 homozygous and by sequence-based typing (SBT) as A*010101,020601. Flow-cytometric (FCM) analysis with 11 human monoclonal antibodies (mAbs) for the A1 molecule confirmed lack of any cell membrane expression of the A*0111N allele. One-dimensional isoelectric focusing (1D-IEF) of total cell lysate from the patient's cells revealed no cell surface and cytoplasmic A1 protein expression, whereas the HLA-A2 molecule was identified by both FCM analysis and 1D-IEF. DNA sequence analysis showed the presence of a synonymous substitution from G to T at position 597 in codon 175. RNA SBT revealed a deletion of 24 bp in exon 3, position 596 through 619, encoding codons 175 through 182 of the HLA-A*0111N allele. The synonymous substitution introduced a new splice site, resulting in an efficient splicing, because no classical A1 protein could be detected in the patient. This alternative splicing prevented the translation into a correct and stable class I molecule expression on the cell surface.

Alleles↗
PubMed2000

Alternative splicing of Drosophila calcium/calmodulin-dependent protein kinase II regulates substrate specificity and activation.

Drosophila calcium/calmodulin-dependent protein kinase II is alternatively spliced to generate multiple isoforms that vary only in a region between the calmodulin-binding domain and the association domain. This variation has been shown to modulate activation of the enzyme by calmodulin. In this study we examine the ability of seven of the Drosophila isoforms to phosphorylate purified protein substrates and to be inhibited by a substrate analog, and the response of six of the isoforms to a mutant form of calmodulin (V91G) that was isolated in a genetic screen. Significant variation in Kms for Eag, a potassium channel, and Adf-1, a transcription factor, were found. In the case of the a peptide inhibitor, AC3I, there were significant variations in Ki between isoforms. Kact for V91G calmodulin was increased for all of the isoforms. In addition, one isoform, RI, exhibited a lower Vmax when assayed with this mutant CaM. These results indicate that the variable domain of calcium/calmodulin-dependent protein kinase II is capable of altering the substrate specificity of the catalytic domain and the activation response to calmodulin.

Alternative Splicing↗
PubMed2000

Differential roles of interleukin 15 mRNA isoforms generated by alternative splicing in immune responses in vivo.

At least two types of interleukin (IL)-15 mRNA isoforms are generated by alternative splicing at the 5' upstream of exon 5 in mice. To elucidate the potential roles of IL-15 isoforms in immune responses in vivo, we constructed two groups of transgenic mice using originally described IL-15 cDNA with a normal exon 5 (normal IL-15 transgenic [Tg] mice) and IL-15 cDNA with an alternative exon 5 (alternative IL-15 Tg mice) under the control of an MHC class I promoter. Normal IL-15 Tg mice constitutionally produced a significant level of IL-15 protein and had markedly increased numbers of memory type (CD44(high) Ly6C(+)) of CD8(+) T cells in the LN. These mice showed resistance to Salmonella infection accompanied by the enhanced interferon (IFN)-gamma production, but depletion of CD8(+) T cells exaggerated the bacterial growth, suggesting that the IL-15-dependent CD8(+) T cells with a memory phenotype may serve to protect against Salmonella infection in normal IL-15 Tg mice. On the other hand, a large amount of intracellular IL-15 protein was detected but hardly secreted extracellularly in alternative IL-15 Tg mice. Although most of the T cells developed normally in the alternative IL-15 Tg mice, they showed impaired IFN-gamma production upon TCR engagement. The alternative IL-15 transgenic mice were susceptible to Salmonella accompanied by impaired production of endogenous IL-15 and IFN-gamma. Thus, two groups of IL-15 Tg mice may provide information concerning the different roles of IL-15 isoforms in the immune system in vivo.

Alternative Splicing↗
PubMed2001

Regulation of alternative splicing of human tau exon 10 by phosphorylation of splicing factors.

Tau is a microtubule-associated protein whose transcript undergoes regulated splicing in the mammalian nervous system. Exon 10 of the gene is an alternatively spliced cassette that is adult-specific and encodes a microtubule-binding domain. Mutations increasing the inclusion of exon 10 result in the production of tau protein which predominantly contains four microtubule-binding repeats and were shown to cause frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). Here we show that exon 10 usage is regulated by CDC2-like kinases CLK1, 2, 3, and 4 that phosphorylate serine-arginine-rich proteins, which in turn regulate pre-mRNA splicing. Cotransfection experiments suggest that CLKs achieve this effect by releasing specific proteins from nuclear storage sites. Our results show that changing pre-mRNA-processing pathways through phosphorylation could be a new therapeutic concept for tauopathies.

Alternative Splicing↗