Detect the Different Isoforms Using GeneChip Human Exon 1.0 ST Arrays

2009 ◽  
Author(s):  
Mi-Chia Ma ◽  
Hsiao-Fang Lin ◽  
Ying Xu
Keyword(s):  
Human Exon

Synthesis of pathological and nonpathological human exon 1 huntingtin

2010 ◽  
pp. n/a-n/a
Author(s):  
David Singer ◽  
Thomas Zauner ◽  
Maika Genz ◽  
Ralf Hoffmann ◽  
Thole Zuchner
Keyword(s):  
Human Exon ◽  
Exon 1

Identification of Alternative Splicing Changes in Erythroid Differentiation Using Human Exon Arrays.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1707-1707
Author(s):  
Miki L. Yamamoto ◽  
Jeong-Ah Kang ◽  
Josh A. Arribere ◽  
Amittha Wickrema ◽  
John G. Conboy
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Erythroid Differentiation ◽  
Transcriptional Level ◽  
Rt Pcr ◽  
Erythroid Progenitor ◽  
Array Data ◽  
Exon Arrays ◽  
Human Exon ◽  
A Genome

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.

scholarly journals Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays

2008 ◽  
Vol 10 (1) ◽  
pp. 50-57 ◽  
Author(s):  
Sameer Jhavar ◽  
Alison Reid ◽  
Jeremy Clark ◽  
Zsofia Kote-Jarai ◽  
Timothy Christmas ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Expression Profiling ◽  
Human Prostate ◽  
Human Prostate Cancer ◽  
Human Exon

scholarly journals The complete local genotype–phenotype landscape for the alternative splicing of a human exon

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Philippe Julien ◽  
Belén Miñana ◽  
Pablo Baeza-Centurion ◽  
Juan Valcárcel ◽  
Ben Lehner
Keyword(s):  
Alternative Splicing ◽  
Human Exon

scholarly journals Structure of the glucocorticoid receptor (NR3C1) gene 5′ untranslated region: identification, and tissue distribution of multiple new human exon 1

2005 ◽  
Vol 35 (2) ◽  
pp. 283-292 ◽  
Author(s):  
Jonathan D Turner ◽  
Claude P Muller
Keyword(s):  
Glucocorticoid Receptor ◽  
Untranslated Region ◽  
Splice Variants ◽  
Splice Acceptor Site ◽  
Specific Expression ◽  
Exon 2 ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Human Exon ◽  
Exon 1

The 5′ untranslated region (UTR) of the glucocorticoid receptor (GR) plays a key role in determining tissue-specific expression and protein isoforms. Analysis of the 5′ UTR of the human GR (hGR) has revealed 11 splice variants of the hGR exon 1, based on seven exon 1s, four of which (1-D to 1-F and 1-H) were previously unknown. All of the exon 1 variants have unique splice donor sites and share a common exon 2 splice acceptor site. Due to an upstream in-frame TGA stop codon the predicted translation from all splice variants is identical. The four new exon 1s show remarkable similarity with their rat homologues. Exon 1-D starts and finishes 17 and 36 bp upstream of the corresponding ends of the rat exon 14. Exon 1-E is only 6 bp longer than its homologue exon 15. Exon 1-F contains two short inserts of 11 and 6 bp when compared with the rat 17. 1-H is 18 bp longer than the corresponding rat 111. In addition to these new exons, we found that the human exon 1-C occurs as three distinct splice variants, covering the region homologous to the rat exons 19 and 110. All of the alternative hGR exons 1s presented here were found to be transcribed in human tissue. The human hippocampus expresses mRNA of all the exon 1 variants, while the expression of the other exon 1s seems to be tissue specific. While exon 1-D is only in the hippocampus, exons 1-E and 1-F are also detected in the immune system, and exon 1-H additionally in the liver, lung and smooth muscle. The 5′ region of the hGR is more complex than previously thought, and we suggest that each of these untranslated first exons have a distinct proximal promoter region, providing additional depth to the mechanisms available for tissue-specific expression of the hGR isoforms.

scholarly journals High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Junwen Wang ◽  
Hui Jiang ◽  
Guanyu Ji ◽  
Fei Gao ◽  
Mingzhi Wu ◽  
...  
Keyword(s):  
High Resolution ◽  
Bisulfite Sequencing ◽  
Human Exon ◽  
Hybridization Capture

Alternate Splicing Is a Frequent Event and Impacts Clinical Outcome in Myeloma: A High-Density Exon Array Analysis of Uniformly Treated Newly-Diagnosed Myeloma Patients

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 498-498 ◽  
Author(s):  
Nikhil C. Munshi ◽  
Cheng Li ◽  
Stephane Minvielle ◽  
Samir B Amin ◽  
Philippe Moreau ◽  
...  
Keyword(s):  
Overall Survival ◽  
Amyloid Beta ◽  
Exon Array ◽  
Newly Diagnosed ◽  
Alternate Splicing ◽  
Array Analysis ◽  
Exon 2 ◽  
Array Data ◽  
Human Exon ◽  
Exon 10

Abstract Alternate splicing is an important post translational change that alters specificity of gene function. Misregulation of alternative splicing has been implicated in number of disease processes including cancer. We have here analyzed alternate splicing in myeloma using high throughput exon array analysis. The GeneChip Human Exon 1.0 ST Arrays used in this investigation not only provides information on expression levels for genes, but as the probe sets are spread evenly over each exon, the array data also provides information on presence of each exon and identify recurrent alternately spliced genes. We conducted a study in series of 170 newly-diagnosed patients with multiple myeloma treated homogeneously in tandem transplantation IFM trials. RNA isolated from CD138 purified MM cells collected at the time of diagnosis were analyzed using the GeneChip Human Exon 1.0 ST Arrays. The dChip software was modified to analyze exon array data. We first normalized gene-level expression values across samples, and then identified differentially expressed exons between two sample groups. These exons are candidates for alternatively splicing events. We observed over 100 genes with candidate alternate splicing events, which have up or down-regulation of an exon relative to the baseline group in more than 20% patients. Dividing the group based on response, 52 alternately spliced exons were identified as influencing response to therapy. The genes and their exons with highest frequency of alternate splicing were CD79A exon 5 and 6, EDNRB exon 2, RASSF1 exon 8, CD1d exon9, TGFBetaRII exon 1, Calmin exon2, CEACAM1 exon 7, MADH1 exon 7, TBX5 exon 2, Amyloid beta exon 14, Nit protein 2 exon 10, Thymidylate synthetase exon 7. Amongst these genes, 32 genes had the most influence on response with over 50% differential frequency in patients achieving CR. Similarly we have identified 85 alternately spliced genes as influencing overall survival between groups divided by less than or more than 48 month survival. The genes with highest frequency of alternate splicing were NOTCH2 exon 18, CXCL3 exon 8, CD9 exon 3 Calmin exon 2, TIMELESS exon 12, SPOUTY homolog 1 exon 4, Amyloid beta exon 14, Nit protein 2 exon 10, Cyclin A2 exon7, lymphocyte antigen 6 exon 7. Forty-nine genes within this group had the most influence on overall survival. Number of spliced variants were shared between both response and survival groups suggesting their biological and functional significance. Further validation of these alternate splicing is under investigations. This study highlights significant frequency of alternate splicing and points to the need for evaluation of not only the expression level of genes but also post translational modifications. The genes identified here are important target for therapy as well as possible immune modulation.

scholarly journals HEXEvent: a database of Human EXon splicing Events

2012 ◽  
Vol 41 (D1) ◽  
pp. D118-D124 ◽  
Author(s):  
Anke Busch ◽  
Klemens J. Hertel
Keyword(s):  
Human Exon ◽  
Exon Splicing

Possible role of nucleotide correlations between human exon junctions

Gene ◽  
2007 ◽  
Vol 393 (1-2) ◽  
pp. 81-86 ◽  
Author(s):  
Piva Francesco ◽  
Principato Giovanni
Keyword(s):  
Human Exon ◽  
Exon Junctions
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