Medium Throughput Analysis of Alternative Splicing by Fluorescently Labeled RT-PCR

Author(s):  
Ryan Percifield ◽  
Daniel Murphy ◽  
Peter Stoilov
1997 ◽  
Vol 48 (2) ◽  
pp. 298-304 ◽  
Author(s):  
Claire Gavériaux-Ruff ◽  
Jean Peluso ◽  
Katia Befort ◽  
Frédéric Simonin ◽  
Christelle Zilliox ◽  
...  

2008 ◽  
Vol 9 (1) ◽  
pp. 313 ◽  
Author(s):  
Michael C Ryan ◽  
Barry R Zeeberg ◽  
Natasha J Caplen ◽  
James A Cleland ◽  
Ari B Kahn ◽  
...  

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1707-1707
Author(s):  
Miki L. Yamamoto ◽  
Jeong-Ah Kang ◽  
Josh A. Arribere ◽  
Amittha Wickrema ◽  
John G. Conboy

Abstract Terminal erythroid differentiation is accompanied by extensive structural remodeling as the cell enucleates and eventually assumes the biconcave disk morphology of the mature cell. Previous studies have documented many changes at the transcriptional level essential for erythroid differentiation. Changes in erythroid gene expression also occur at the level of pre-mRNA alternative splicing: the activation of 4.1R (EPB41) exon 16 splicing in late erythroblasts increases 4.1R affinity for spectrin-actin and mechanically strengthens the plasma membrane. We hypothesize that analogous changes in alternative splicing affect the structure and function of other erythroid proteins. To identify additional alternative splicing switches in erythroid genes, a genome-wide exon expression analysis was carried out using the new Affymetrix Human Exon 1.0 ST Array. Unlike traditional gene expression microarrays, this array has single exon resolution and can detect changes in expression due to alternative splicing. Samples for array analyses were prepared from RNA of human erythroid progenitor cells grown in culture for 7, 10, and 14 days, corresponding to basophilic, polychromatic, and orthochromatic stages. Analysis of this exon array data confirmed that 4.1R exon 16 splicing was activated in day 14 cells, and that a known inhibitor of exon 16 splicing, hnRNP A1, was down-regulated in coordination with the 4.1R splicing switch. As another positive control, we confirmed in array data the expression of a known erythroid-specific 3′ end in beta-spectrin mRNA in all three time points of erythroblasts, while array data from muscle tissue showed expression of only the non-erythroid 3′ end of beta-spectrin. Array data is now being analyzed to identify new cases of alternative splicing during erythropoiesis, and confirmation of several candidate splicing switches by RT-PCR and quantitative PCR is under way. A number of genes, including PIK3R1, SLC12A6, and TNPO2, show changes in alternative 5′ first exon usage during late erythropoiesis. A splicing change involving an internal cassette exon in MBNL2, which encodes a splicing regulator, was identified by array data and confirmed by RT-PCR. In addition, overall gene expression analyses confirm up-regulation of known genes expressed during erythroid differentiation, including Band 3, GLUT1, ALAS2, and BCL2L1. This preliminary analysis demonstrates the application of exon arrays toward the identification of splicing switches that occur during differentiation of human erythroblasts. Further validation of putative alternative splicing events is in progress, and investigation of the regulation of the validated events and the physiological implications of the predicted changes in the proteins will be pursued in the future.


2017 ◽  
Author(s):  
Christopher J. Green ◽  
Matthew R. Gazzara ◽  
Yoseph Barash

AbstractAnalysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret, and experimentally validate. To address these challenges, We developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex (non-binary) splicing variations. Using a matching primer design algorithm it also suggests users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis.Availability: Program and code will be available at http://majiq.biociphers.org/majiq-spel


2018 ◽  
Vol 1 (3) ◽  
Author(s):  
Xuyang Bai ◽  
Baoai Wu ◽  
Junzhen Shi ◽  
Infeng Zhao

Objective Obesity is one of a world-wide chronic diseases, which is the leading cause of cancer, T2D, cardiovascular disease other metabolic complications. Aerobic exercise as a moderate intervention, has potential mechanisms for the loss weight. Lipin1 as a key regulator of lipid metabolism is a member of the Lipin family. Through alternative splicing, Lipin1 exists two isoforms,Lipin1α is mostly expressed in preadipocytes during the initial stages of differentiation, whereas the Lipin1β mainly expressed in mature adipocytes, and is responsible for lipogenesis and adipocyte hypertrophy.The aim of our present study was to investigate the effect of aerobic exercise on the levels of Lipin1α、Lipin1β and splicing factor SFRS10. Methods C57BL/6 mice were randomly assigned to control group(C, n=20) and obesity control group (O, n=20). After 4weeks,mice were further assigned to normal control group (NC,n=10),and control exercise group (CE,n=10),O group ( O, n = 10) and obesity exercise group (OE, n = 10),CE and OE were on aerobic exercised for 8 weeks. RT-PCR was generated to detect Lipin1α、Lipin1βand SFRS10 mRNA expression. Results The results suggest that the level of lipin1α mRNA was decreased in obesity group. With exercise, levels in CE and OE increased. Furthermore, Lipin1β was increased in obesity group and decrease after aerobic exercise in both CE and OE. We also demonstrated the SFRS10, which can bind to lipin1 exon8 and regulate Lipin1 alternative splicing, had a lower ex pression in obesity group and higher expression in CE and OE.  Conclusions  Our data suggest that aerobic exercise can reduce body weight by influencing lipin1 pre-mRAN alternative splicing, and change the expression of two isoforms. Besides aerobic exercise can also affect SFRS10 mRNA Levels and change the expression of Lipin1 isoform.


2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e15641-e15641
Author(s):  
X. Geng

e15641 Background: To investigate the changes of hTERT alternative splicing variants pattern in gastric cancer, precancerous lesions and normal gastric mucosa tissue. Methods: Three alternative splicing sites (α, β, γ) were selected and designed PCR primer. The expression of 8 hTERT alternative splicing variants (ASVs) in gastric cancer, precancerous lesions and normal gastric mucosa were detected by Semi-nested RT-PCR. The expression of β-site remaining ASV (β+ASV) in specimens of gastric cancer and specimens of precancerous lesions was detected by SYBER Green real-time PCR. Telomerase enzyme activity was evaluated associated with the different hTERT ASVs. Results: The positive rate of active full-length (α+β+γ+ ) ASV was significantly higher in gastric cancer than in precancerous lesions and normal mucosa (94.7% vs. 40.0% and 0, P<0.05). The positive rates of other ASVs were not different among the 3 groups(P>0.05). The positive rates of β+ ASVs (including α+β+γ+ASV, α-deletion ASV, γ-deletion ASV, αγ-deletion ASV) were 11.1% in normal mucosa,40.0% in precancerous lesions and 94.7% in gastric cancer (P<0.05). SYBR Green real-time RT-PCR showed that the expression level of β+ASV was 6.99 times higher in gastric cancer than in precancerous lesions. Further, increased telomerase enzyme activity was only associated with expression of the full-length hTERT isoform. Conclusions: hTERT alternative splicing pattern is different during gastric carcinogenesis. β+ASV was widely expressed in gastric carcinogenesis and may provide some information for diagnosis of gastric cancer or precancerous lesions. The gene expression patterns of hTERT alternative splicing variants may provide some useful information for diagnosis of gastric cancer and precancerous lesions. No significant financial relationships to disclose.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1189-1189
Author(s):  
Joellen H. H. Lin ◽  
Mathieu Garand ◽  
Branislava Zagorac ◽  
Anastassia Filipieva ◽  
Marlys L Koschinsky ◽  
...  

Abstract Abstract 1189 Thrombin-activatable fibrinolysis inhibitor (TAFI) is a basic carboxypeptidase zymogen that plays important roles in modulation of fibrinolysis and inflammation. Activated TAFI (TAFIa) removes carboxyl-terminal lysine and/or arginine residues from substrates such as partially-degraded fibrin, cell-surface plasminogen receptors, bradykinin, the anaphylatoxins C3a and C5a, and thrombin-cleaved osteopontin. The plasma pool of TAFI arises from expression of its gene (CPB2) in the liver. However, CPB2 is expressed in other locations including platelets (arising from expression in megakaryocytes), monocytes, and macrophages. An additional source of CPB2 expression has been shown to be the hippocampus; this TAFI variant was reported to be expressed from a CPB2 mRNA in which (i) exon 7 had been skipped resulting in an in-frame loss of 37 codons and (ii) alternative splicing had occurred in exon 11 resulting in a frameshift that deletes the final 42 codons and introduces a novel 16-amino acid carboxyl-terminus. Most recently, skipping of exon 7 has been reported in HepG2 (human hepatocellular carcinoma) cells, a phenomenon that appears to play a role in balancing selection at the CPB2 locus in the human population. As much as 12.5% of the CPB2 transcript in HepG2 cells was reported to lack exon 7. Accordingly, we have characterized, using RT-PCR, molecular cloning, and quantitative RT-PCR, the splicing patterns of CPB2 mRNA in a variety of cell types. We examined RNA isolated from human liver, HepG2 cells, the megakaryocytoid cell line Dami, platelets, the monocytoid cell line THP-1, and human cerebral cortex and cerebellum. We found evidence for alternative splicing/exon skipping in all cell types tested. All cells contained CPB2 mRNA lacking exon 7. Only platelets, cortex, and cerebellum CPB2 mRNA featured alternatively spliced exon 11, and all cDNA clones identified that contained exon 11 alternative splicing also lacked exon 7. Quantitative analysis of the proportion of total CPB2 transcripts that lack exon 7 showed that HepG2 cells had almost 10% exon 7-less transcripts but all other cell types tested had far lower proportions, ranging from 1% (Dami cells, peripheral blood mononuclear cells and cerebellum) to less than 0.1% (liver, THP-1 cells, platelets). Studies of CPB2 expressed in the hippocampus suggested that the variant lacking exon 7 and featuring alternative splicing in exon 11 encodes a protein that is localized in the endoplasmic reticulum of neural cells and that possesses endopeptidase activity against amyloid precursor protein. To test the functional properties of the TAFI proteins encoded by the TAFI variants, we transfected baby hamster kidney cells with expression plasmids encoding variants lacking exon 7, alternatively spliced exon 11, or both variations. Interestingly, unlike wild-type recombinant TAFI in these cells, the variant proteins could not be secreted, despite the presence of an intact signal peptide in each. Western blot analyses of transfected cell lysates revealed immunoreactive bands between 40 and 45 kDa, consistent with hypoglycosylated TAFI; lysates of cells expressing wild-type TAFI contained a 45 kDa species and a 60 kDa mature preproprotein. We therefore propose that the variant proteins are aberrantly folded and thus do not exit the ER. Notably, none of the variant proteins could be activated by thrombin-thrombomodulin and they did not show activity in a specific functional assay for TAFIa. Deletion of exon 7-encoded residues removes two surface α-helices and a single internal β-strand from the TAFI structure. Alternative splicing in exon 11 deletes a critical catalytic residue (Glu363). It is therefore not surprising that the variants are aberrantly folded, are not secretable, and lack TAFIa activity. It is also difficult to envisage how such a protein could acquire endopeptidase activity. We therefore speculate that variant TAFI resulting from exon skipping and alternative splicing may act as a chaperone for the presumptive peptidase that recognizes amyloid precursor protein. Moreover, full-length TAFI is expressed in the brain and may regulate brain-expressed tPA and plasminogen to influence neural function. Finally, it is possible that, under certain circumstances, the extent of exon skipping/alternative splicing is sufficient to impact the secretion of functional TAFI from liver or other cell types. Disclosures: No relevant conflicts of interest to declare.


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