Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells
ABSTRACT Alternative splicing provides a versatile mechanism of gene regulation, which is often subverted in disease. We have used customized oligonucleotide microarrays to interrogate simultaneously the levels of expression of splicing factors and the patterns of alternative splicing of genes involved in tumor progression. Analysis of RNAs isolated from cell lines derived from Hodgkin lymphoma tumors indicate that the relative abundance of alternatively spliced isoforms correlates with transformation and tumor grade. Changes in expression of regulators were also detected, and a subset sample was confirmed at the protein level. Ectopic expression of neuron-specific splicing regulatory proteins of the Nova family was observed in some cell lines and tumor samples, correlating with expression of a neuron-specific mRNA isoform of JNK2 kinase. This microarray design can help assess the role of alternative splicing in a variety of biological and medical problems and potentially serve as a diagnostic tool.
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ABSTRACT: Digitalis purpurea (D. purpurea) is one of the most important medicinal plants and is well known in the treatment of heart failure because of the cardiac glycosides that are its main active compounds. However, in the absence of strand specific sequencing information, the post-transcriptional mechanism of gene regulation in D. purpurea thus far remains unknown. In this study, a strand-specific RNA-Seq library was constructed and sequenced using Illumina HiSeq platforms to characterize the transcriptome of D. purpurea with a focus on alternative splicing (AS) events and the effect of AS on protein domains. De novo RNA-Seq assembly resulted in 48,475 genes. Based on the assembled transcripts, we reported a list of 3,265 AS genes, including 5,408 AS events in D. purpurea. Interestingly, both glycosyltransferases and monooxygenase, which were involved in the biosynthesis of cardiac glycosides, are regulated by AS. A total of 2,422 AS events occurred in coding regions, and 959 AS events were located in the regions of 882 unique protein domains, which could affect protein function. This D. purpurea transcriptome study substantially increased the expressed sequence resource and presented a better understanding of post-transcriptional regulation to further facilitate the medicinal applications of D. purpurea for human health.PLoS ONE 08/2014; 9(8):e106001. DOI:10.1371/journal.pone.0106001 · 3.53 Impact Factor
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ABSTRACT: The accurate expression of the genetic information is regulated by processes like mRNA splicing, proposed after the discoveries of Phil Sharp and Richard Roberts, who demonstrated the existence of intronic sequences, present in almost every structural eukaryotic gene, which should be precisely removed. This intron removal is called “splicing”, which generates different proteins from a single mRNA, with different or even antagonistic functions. We currently know that alternative splicing is the most important source of protein diversity, given that 70% of the human genes undergo splicing and that mutations causing defects in this process could originate up to 50% of genetic diseases, including cancer. When these defects occur in genes involved in cell adhesion, proliferation and cell cycle regulation, there is an impact on cancer progression, rising the opportunity to diagnose and treat some types of cancer according to a particular splicing profile.Medicina Clínica 04/2014; DOI:10.1016/j.medcli.2014.02.021 · 1.25 Impact Factor
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ABSTRACT: Systematic genetic and epigenetic alterations occurring in almost all cancer cells result in the ectopic expression of a variety of tissue-specific potent regulatory factors. This review sheds light on a new aspect of cancer based on the integration of the 'out of context' activity of tissue-restricted genes into the biology of cancer cells. A systematic screen for the ectopic activation of tissue-restricted genes in a variety of cancers has revealed that many normally silent genes are expressed in tumours of all origins. This aberrant gene activation not only could be used as a source of biomarkers, but also, in several cases, reveals clear oncogenic mechanisms associated with the corresponding ectopically expressed factors. The characteristic of all cancer cells, which systematically reprogram tissue-specific gene expression and activate silent genes, can be exploited to develop new anticancer strategies aiming at the detection of malignant states, the prediction of their evolution and drug sensitivity and the discovery of new therapeutic approaches.Current opinion in oncology 11/2013; DOI:10.1097/CCO.0000000000000032 · 3.76 Impact Factor