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 1,153 records · Page 64Linked to original sources

PubMed1996

Identification of an alternatively spliced transcript of equine interleukin-1 beta.

Using lipopolysaccharide (LPS)-stimulated equine peripheral blood mononuclear cell (PBMC) cDNA as a template, we performed polymerase chain reaction (PCR) amplification with equine interleukin-1 beta (IL-1 beta) specific primers. Electrophoresis of the PCR product on agarose gel revealed an additional smaller fragment that hybridized with an equine IL-1 beta cDNA probe. Sequencing of this fragment demonstrated that it was shorter than normal equine IL-1 beta cDNA by 162 nucleotides, which corresponded to exon 5 of the human and murine IL-1 beta genes. The deletion of 162 nucleotides did not result in a frame shift but spliced out the putative exon 5 of the IL-1 beta gene which includes the cleavage site for the IL-1 beta converting enzyme (ICE) in human and murine IL-1 beta. Expression of the alternatively spliced IL-1 beta transcript in PBMC was also detected after stimulation with other compounds. These results clearly indicate the existence of an alternatively spliced IL-1 beta transcript in equine PBMC.

Alternative Splicing↗

PubMed2005

Genomic structure, alternative splicing and tissue expression of rFrp/sFRP-4, the rat frizzled related protein gene.

Secreted frizzled related proteins (sFRP) are regulators of Wnt signaling pathways that play central roles in developmental processes and oncogenesis. Various sFRP genes have been cloned from different tissues and implicated in diverse biological activities. rFrp, the rat homologue of sFRP-4, was initially identified as being upregulated in mutant p53-induced cellular transformation. Here, we report on the isolation of five novel splice variants, rFrp/sFRP-4 II, II, III, IVa and IVb. The complete rFrp/sFRP-4 genomic structure spans over 31 kb covering 9 exons. Except for the variant IVb, which was derived from IVa by alternative polyadenylation signal, variants I to IVa were alternatively spliced to different exons in the 3'end of mRNA and resulted in transcripts with truncated open reading frame. The deduced proteins of the variants had truncated C-termini, however, the two key functional protein domains, the cysteine-rich domain and the netrin-like domain of the isoforms, were not altered. In addition, different transcriptional initiation sites were found with variants II and IV, implying that these variants may be regulated differently from the rFrp/sFRP-4. RT-PCR analysis showed that these splice variants displayed different patterns of tissue-specific expression. Northern blot analysis revealed that the rFrp/sFRP-4 is most abundant in the ovary. Taken together, our findings suggest that alternative splicing of rFrp/sFRP-4 plays a role in regulating tissue-specific expression. The truncated C terminals of rFrp/sFRP-4 variants may confer structural specificity and hence exert different biological functions in different tissues. Characterization of these novel splice variants should help to elucidate the function of the sFRP family gene.

Alternative Splicing↗

PubMedDate not supplied

Alternative splicing within the ligand binding domain of the human constitutive androstane receptor.

The human constitutive androstane receptor (hCAR; NR1I3) is a member of the nuclear receptor superfamily. The activity of hCAR is regulated by a variety of xenobiotics including clotrimazole and acetaminophen metabolites. hCAR, in turn, regulates a number of genes responsible for xenobiotic metabolism and transport including several cytochrome P450s (CYP 2B5, 2C9, and 3A4) and the multidrug resistance-associated protein 2 (MRP2, ABCC2). Thus, hCAR is believed to be a mediator of drug-drug interactions. We identified two novel hCAR splice variants: hCAR2 encodes a receptor in which alternative splice acceptor sites are utilized resulting in a 4 amino acid insert between exons 6 and 7, and a 5 amino acid insert between 7 and 8, and hCAR3 encodes a receptor with exon 7 completely deleted resulting in a 39 amino acid deletion. Both hCAR2 and hCAR3 mRNAs are expressed in a pattern similar to the initially described MB67 (hCAR1) with some key distinctions. Although the levels of expression vary depending on the tissue examined, hCAR2 and hCAR3 contribute 6-8% of total hCAR mRNA in liver. Analysis of the activity of these variants indicates that both hCAR2 and hCAR3 lose the ability to heterodimerize with RXR and lack transactivation activity in cotransfection experiments where either full-length receptor or GAL4 DNA-binding domain/CAR ligand binding domain chimeras were utilized. Although the role of hCAR2 and hCAR3 is currently unclear, these additional splice variants may provide for increased diversity in terms of responsiveness to xenobiotics.

Alternative Splicing↗

PubMed2003

Plasma levels of fibronectin bearing the alternatively spliced EIIIB segment are increased after major trauma.

Using Western-blot analysis and enzyme-linked immunosorbent assay (ELISA) of N-deglycosylated samples, we have observed that plasma levels of fibronectin (FN) bearing the alternatively spliced EIIIB segment (EIIIB(+) FN) increase in patients after admission to the intensive-care unit (ICU) for acute major trauma. Although not increased at the first sampling ("0 hour"), taken within 24 hours of ICU admission, levels measured 24, 48, and 72 hours later were significantly increased compared with levels obtained in healthy controls. Furthermore, average concentrations at these latter time points were significantly increased relative to the 0-hour sampling. EIIIB(+) FN levels then decreased in plasma samples taken 1 month after hospital discharge, such that no significant difference was found between ELISA-measured values at this time and 0 hour or control values. On the basis of comparisons with previous measurements in these samples, it is apparent that after acute major trauma, circulating levels of soluble EIIIB(+) FN exhibit temporal changes that are qualitatively similar to those encountered for FN isoforms bearing the alternatively spliced EIIIA segment (EIIIA(+) FN), yet different from those observed for the total pool of circulating FN. This is the first report of measurement of FN in clinical plasma samples with antibodies specific for the highly conserved EIIIB segment. Like EIIIA(+) forms of FN, EIIIB(+) FNs are recognized as soluble bloodborne markers for vascular tissue injury.

Adult↗

PubMed2003

An alternative splice form of Mdm2 induces p53-independent cell growth and tumorigenesis.

The Mdm2 gene is amplified in approximately one-third of human sarcomas and overexpressed in a variety of other human cancers. Mdm2 functions as an oncoprotein, in part, by acting as a negative regulator of the p53 tumor suppressor protein. Multiple spliced forms of Mdm2 transcripts have been observed in human tumors; however, the contribution of these variant transcripts to tumorigenesis is unknown. In this report, we isolate alternative splice forms of Mdm2 transcripts from sarcomas that spontaneously arise in Mdm2-overexpressing mice, including Mdm2-b, the splice form most commonly observed in human cancers. Transduction of Mdm2-b into a variety of cell types reveals that Mdm2-b promotes p53-independent cell growth, inhibits apoptosis, and up-regulates the RelA subunit of NFkappaB. Furthermore, expression of Mdm2-b induces tumor formation in transgenic mice. These results identify a p53-independent role for Mdm2 and determine that an alternate spliced form of Mdm2 can contribute to formation of cancer via a p53-independent mechanism. These findings also provide a rationale for the poorer prognosis of those patients presenting with tumors harboring multiple Mdm2 transcripts.

Alternative Splicing↗

PubMed1998

An alternatively spliced form of apobec-1 messenger RNA is overexpressed in human colon cancer.

BACKGROUND & AIMS: Apobec-1 is an RNA-specific cytidine deaminase whose forced overexpression in transgenic animals is associated with hepatic carcinogenesis. Apobec-1 messenger RNA (mRNA) undergoes alternative splicing, generating a catalytically inactive peptide, apobec-T. We have examined apobec-1 gene expression in human gastrointestinal tumors and in colon cancer-derived cell lines. METHODS: Levels of the full-length (apobec-1) and alternatively spliced (apobec-T) mRNAs were measured by RNase protection assay, and apobec-T distribution was determined by immunocytochemical localization. RESULTS: Apobec-1 mRNA was detectable in normal and colon cancer tissue, metastatic nodules, and certain colon cancer-derived cell lines. Apobec-T mRNA abundance was increased an average of 3.5-fold in colon cancers compared with paired control tissue (range, 0.5-14-fold). Immunocytochemical analysis showed apobec-T expression in normal fetal and adult colon and in gastric and small intestinal adenocarcinomas, colonic tubular adenomas, and both primary and metastatic colonic tumors. Overexpression of apobec-T in a tetracycline-responsive cell line decreased cellular proliferation. CONCLUSIONS: Apobec-T is expressed in normal, adenomatous, and cancerous gastrointestinal tissues, and levels of the mRNA encoding this peptide are significantly increased in colon cancer. Although its relationship to colon carcinogenesis has not been defined, the regulated overexpression of apobec-T is associated with an altered growth phenotype.

3T3 Cells↗

PubMed2005

Identification and functional characterization of an alternative splice variant within the fourth exon of human nanog.

Nanog, a homeodomain (HD) transcription factor, plays a critical role in the maintenance of embryonic stem (ES) cell self-renewal. Here, we report the identification of an alternatively-spliced variant of nanog. This variant lacked a stretch of amino acids (residues 168-183) located between the HD and tryptophan-repeat (WR) of the previously-reported full length sequence, suggesting that the deleted sequence functions as a linker and possibly affects the flexibility of the C-terminal transactivation domain relative to the DNA binding domain. Expression of mRNA encoding the splice variant, designated as nanog-delta 48, was much lower than that of the full length version in human ES cells. The ratio of nanog-delta 48 transcript to full length transcript increased, however, in multipotent adult progenitor cells. EMSA analysis revealed that both forms of Nanog were able to bind a nanog binding sequence with roughly the same affinity. A reporter plasmid assay also showed that both variants of nanog modestly repressed transactivation of gata-4, whose expression is proposed to be inhibited by nanog, with comparable potency. We conclude that, despite the difference in primary structure and expression pattern in various stem cells, the alternatively-spliced variant of Nanog has similar activity to that of the full length version.

Alternative Splicing↗

PubMed2002

Detection of circulating prostate tumor cells: alternative spliced variant of PSM induced false-positive result.

RT-nested PCR has been introduced as a highly specific and sensitive assay method to detect the prostate-specific membrane antigen (PSM) mRNA in peripheral blood. However, appreciable percentages of false-positive cases have been reported. Additionally, primer sets reported previously could not discriminate between PSM and PSM', an alternatively spliced variant, mRNA. These isoforms can be produced from a single gene. Switches in alternative splicing patterns are often controlled with strict cell-type or developmental-stage specificity. Therefore, it is most important to discriminate between PSM mRNA and PSM' mRNA. Using our highly specific primer sets, PSM mRNA was detected in 3 of 24 peripheral blood samples of normal male volunteers (12.5%) and was not detected in peripheral blood of 11 normal female volunteers. PSM' mRNA was detected in 5 of 24 peripheral blood samples of normal male volunteers (20.8%) and in 4 of 11 of normal female volunteers (36.4%). PSM' mRNA induced false-positive results, it is important for genetic diagnosis of prostate cancer to discriminate between PSM and PSM' using our primer sets with high specificity. The advances in the uniquely designed primer sets may allow researchers to detect a real PSM mRNA without PSM' mRNA.

Adult↗

PubMed2002

Tenascin-C promotes neurite outgrowth of embryonic hippocampal neurons through the alternatively spliced fibronectin type III BD domains via activation of the cell adhesion molecule F3/contactin.

Tenascin-C is a multimodular glycoprotein that possesses neurite outgrowth-stimulating properties, and one functional site has been localized to the alternatively spliced fibronectin type III domain D. To identify the neuronal receptor that mediates this effect, neighboring pairs of fibronectin type III domains were expressed as hybrid proteins fused to the Fc fragment of human immunoglobulin. These IgFc fusions were tested for neurite outgrowth-promoting properties on embryonic day 18 rat hippocampal neurons, and both the combinations BD and D6 were shown to promote the elongation of the longest process, the prospective axon. Antibodies to the cell adhesion molecule F3/contactin of the Ig superfamily blocked the BD- but not the D6-dependent effect. Biochemical studies using F3/contactin-IgFc chimeric proteins confirmed that the adhesion molecule selectively reacts with the combination BD but not with other pairs of fibronectin type III repeats of tenascin-C. The alternatively spliced BD cassettes are prominently expressed in the developing hippocampus, as shown by reverse transcription PCR, and colocalize with F3 expression during perinatal periods when axon growth and the establishment of hippocampal connections take place. We conclude that F3/contactin regulates axon growth of hippocampal neurons in response to tenascin-C.

Alternative Splicing↗

PubMed2006

Multiple alternative splicing of mouse Dmrt1 during gonadal differentiation.

Evolutionarily conserved Dmrt1 encodes a transcriptional regulator that is expressed exclusively in the gonads and is required for testis differentiation. Here we report that four transcripts of the mouse Dmrt1 were generated in developing gonads and adult testis by alternative splicing. Dmrt1 a encodes the known protein with 374 amino acids. Dmrt1 b, Dmrt1 c, and Dmrt1 d encode predicted proteins with 212, 257, and 194 amino acids, respectively. Dmrt1 a2 and Dmrt1 a3 have anterior alternative polyadenylation signals in 3'UTR than the known Dmrt1 transcript (Dmrt1 a1). Dmrt1 a2 lacks 18 nucleic acids in 3'UTR. Interestingly, Dmrt1 b lacks exon5, Dmrt1 c lacks exon3, and Dmrt1 d lacks both exon1 and exon2 which encode DM domain. RT-PCR showed that all of Dmrt1 transcripts were only detectable in adult testis. However, during gonadogenesis, the multiple alternatively spliced transcripts all had gonad-specific and sexually dimorphic expression profiles. Northern blot and real time fluorescent quantitative RT-PCR further indicated that the expression of Dmrt1 a was dominantly higher than those of Dmrt1 b, c, and d, although they showed a similar up and down pattern of expression during embryo development. The expression of Dmrt1 transcripts climbed up to a climax at 13.5dpc in both male and female gonad. Afterwards, expression in male gonad decreased to a low level and maintained, whereas female one reduced rapidly until undetectable in adult ovary. These results provide new insight into roles of regulation at level of splicing of the Dmrt1 in governing sex differentiation.

Alternative Splicing↗

PubMed1994

Differential expression of alternatively spliced fibronectin in normal and wounded rat corneal stroma versus epithelium.

PURPOSE: The polymerase chain reaction was used to examine fibronectin (FN) expression during corneal scrape wounding with specific attention to the presence, absence, or gross changes of alternatively spliced FN as differentially expressed in the corneal stroma versus the epithelium in normal and wounded tissue. METHODS: Specific FN cDNA sequences were synthesized from rat cornea with total RNA and were amplified using various sets of synthetic oligonucleotide primers. RESULTS: The authors observed the presence and sustained the expression of total FN, EIIIA, EIIIB, and V-region FN mRNA in normal and injured corneal stroma for up to 3 weeks after scrape wounding. In contrast, complementary overlying epithelial samples were virtually devoid of FN message. CONCLUSIONS: These data suggest that functionally different, alternatively spliced FN isoforms may be involved both in the maintenance of the normal cornea and in wound healing, and that their synthesis occurs in situ principally by the stroma rather than by the epithelium.

Alternative Splicing↗

PubMed1994

Alternative splicing governs sulfation of tyrosine or oligosaccharide on peptidylglycine alpha-amidating monooxygenase.

Peptidylglycine alpha-amidating monooxygenase (PAM) catalyzes the COOH-terminal alpha-amidation of neuro-endocrine peptides through the sequential action of monooxygenase and lyase domains contained within this bifunctional protein. Alternative splicing leads to the expression of soluble and integral membrane bifunctional PAM proteins as well as a soluble monofunctional monooxygenase. In order to determine how alternative splicing affects post-translational modification of PAM proteins, we investigated the sulfation of PAM proteins expressed in stably transfected hEK-293 cells. Metabolic labeling with [35S]SO4(2-) or [35S]methionine and immunoprecipitation demonstrated that [35S]SO4(2-) was efficiently incorporated into PAM proteins that have the noncatalytic exon A region following the monooxygenase domain (PAM-1 and PAM-4) and into a soluble bifunctional PAM protein (PAM-3). Alkaline hydrolysis, radiosequencing, and deglycosylation experiments demonstrated the presence of a sulfated tyrosine (Tyr965) in the COOH-terminal domain of PAM-3 and multiple sulfated O-glycans in the exon A region of PAM-1 and PAM-4. A mutant PAM-3 protein in which Tyr965 was changed to Ala965 (PAM-3/Y965A) was not sulfated and exhibited monooxygenase and lyase activities similar to those of wild type PAM-3. Pulse-chase and temperature block experiments showed that the PAM-3/Y965A protein exits the trans-Golgi network faster than wild type PAM-3. Thus inclusion of exon A results in the sulfation of O-glycans, while elimination of the transmembrane domain results in the sulfation of Tyr965.

Alternative Splicing↗

PubMed1997

Alternative splicing of ClC-6 (a member of the CIC chloride-channel family) transcripts generates three truncated isoforms one of which, ClC-6c, is kidney-specific.

ClC-6 is a protein that structurally belongs to the family of ClC-type chloride channels. We now report the identification of three additional ClC-6 isoforms that are truncated because of alternative splicing. We have isolated, from human K562 cells, four types of ClC-6 cDNAs that encode four distinct ClC-6 protein isoforms. ClC-6a (869 amino acids) corresponds to the previously published ClC-6 protein [Brandt and Jentsch (1995) FEBS Lett. 377, 15-20] and it has a canonical ClC structure. However, ClC-6b (320 amino acids), ClC-6c (353 amino acids) and ClC-6d (308 amino acids) are truncated at their C-termini. Hydropathy-plot analysis indicates that the shortened isoforms contain maximally four (ClC-6b and -6d) or seven (ClC-6c) transmembrane domains. Sequence analysis of a human genomic ClC-6 fragment indicates that the cDNA variability arises from alternative splicing at two different positions: the first alternative site consists of an intron flanked by two alternative donor sites and two alternative acceptor sites, the second being due to an exon that is optionally included or excluded. Reverse-transcription-PCR analysis of ClC-6 expression in human cell lines and tissues shows that the majority (83%) of ClC-6 mRNAs consists of ClC-6a or ClC-6c messengers. Furthermore, in a mouse tissue panel, the ClC-6a mRNA has a relatively broad tissue expression pattern, since it could be detected in brain, kidney, testis, skeletal muscle, thymus and pancreas. In contrast, expression of ClC-6c is more restricted, since it was only detected in kidney.

Alternative Splicing↗

PubMed1995

Analysis of an alternatively spliced exon of the neurofibromatosis type 1 gene in cultured melanocytes from patients with neurofibromatosis 1.

Neurofibromatosis type 1 (NF1) is characterized by clinical features that primarily affect tissues derived from the neural crest (neurofibromas, café-aulait macules). Because aberrant regulation of alternative splicing in the NF1 gene transcript may be of functional significance, cultured melanocytes from café-aulait macules (CALM), as an example of benign NF1 lesions, were examined for the expression of the different alternative splice products of this gene. Both kinds of NF1 messengers (type 1 and 2) were found not only in CALM melanocytes but also in keratinocytes, fibroblasts and blood cells. Except in blood cells, there was a predominance of the type 2 transcript. Melanocytes from NF1 patients and healthy donors showed similar expression patterns under several culture conditions. Our results suggest that the development of CALM does not correlate with a switch in the ratio of type 1 to type 2 NF1 messenger RNA.

Alternative Splicing↗

PubMed1999

An element in the 5' common exon of the NCAM alternative splicing unit interacts with SR proteins and modulates 5' splice site selection.

The neural cell adhesion molecule (NCAM) gene contains an 801 nt exon that is included preferentially in neuronal cells. We have set up an in vitro splicing system that mimics the neuro-specific alternative splicing profile of NCAM exon 18. Splicing regulation is observed using model pre-mRNAs that contain competing 5' or 3' splice sites, suggesting that distinct pathways regulate NCAM 5' and 3' splice site selection. While inclusion of exon 18 is the predom-inant choice in neuronal cells, an element in the 5' common exon 17 improves exon 17/exon 19 splicing in a neuronal cell line. A similar behavior is observed in vitro as the element can stimulate the 5' splice site of exon 17 or a heterologous 5' splice site. The minimal 32 nt sequence of the exon 17 enhancer consists of purine stretches and A/C motifs. Mutations in the purine stretches compromise the binding of SR proteins and decreases splicing stimulation in vitro. Mutations in the A/C motifs do not affect SR protein binding but reduce enhancing activity. Our results suggest that the assembly of an enhancer complex containing SR proteins in a 5' common exon ensures that NCAM mRNAs lacking exon 18 are made in neuronal cells.

Alternative Splicing↗

PubMed2001

Highlights of alternative splicing regulation session: yes, no, maybe--a history of paradigm shifts.

Highlights from the Sixth Annual Meeting of the RNA Society, Banff, Alberta, Canada, 29 May to 3 June 2001. Cooper summarizes the discussions and presentations from the session entitled "Control of Splice Site Selection" held at the Sixth Annual Meeting of the RNA Society. Paradigms are shifting as experiments show that some of the proteins involved in regulating splicing can act as splicing enhancers or repressors, depending on the cellular context. The complex interactions among the ribonucleoproteins (RNPs) and proteins, and the role of cis elements, in controlling cell-specific splicing are highlighted. The importance of properly regulated splicing is emphasized by examples of disease pathologies in which alternative splicing is aberrant.

Alternative Splicing↗

PubMed1998

Loss of a consensus heparin binding site by alternative splicing of latent transforming growth factor-beta binding protein-1.

Latent transforming growth factor-beta binding protein-1 (LTBP-1), plays an important role in controlling localisation and activation of transforming growth factor-beta (TGF-beta). We show that alternative splicing generates a form of mRNA which lacks bases 1277-1435 (termed LTBP-1delta53). The 53 amino acids encoded by these bases include the eighth cysteine of the first cysteine repeat and a consensus heparin binding sequence. Sequencing of genomic clones showed that alternative splicing resulted from the use of an intra-exonic 3' splice acceptor site. The loss of the heparin binding site implies that LTBP-1delta53 will bind to the extracellular matrix less efficiently than LTBP-1.

Alternative Splicing↗

PubMed2006

An alternatively spliced form of Met receptor is tumorigenic.

The Met tyrosine kinase receptor is a widely expressed molecule, which mediates pleiotropic cellular responses following activation by its ligand, hepatocyte growth factor/scatter factor (HGF/SF). Previously, one of the authors identified an alternatively spliced form of Met (Met-SM) that lacked a single exon of a 47-amino-acid segment in the juxtamembrane domain. Here we report that Met-SM is a potent transforming gene in NIH3T3 mouse fibroblast cells. Met-SM-transfected NIH3T3 cells show stronger foci-forming activity than wild type- Met-transfected ones. In addition, Met-SM-transfected NIH3T3 cells form colonies in soft agar and are tumorigenic in athymic nu/nu mice. Furthermore, HGF/SF significantly increases the focus-forming activity of Met-SM comparing to wild type Met. The amount of protein and of tyrosine kinase activity of Met-SM accumulates to a high level following HGF/SF treatment. The accumulation of Met-SM correlated well with its delayed ubiquitination and increased stability. These results are consistent with the important role of the juxtamembrane domain in protein stability of Met receptor and suggest that the alternatively-spliced form may contribute to the development and progression of human cancer.

Alternative Splicing↗